View genomic variant #0000017569

Variant on transcripts

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Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:

• 5' gene flanking
• 5' UTR
• Exon
• Intron
• 3' UTR
• 3' gene flanking

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.

Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.

RNA change: Description of variant at RNA level (following HGVS recommendations).

• r.123c>u
• r.? = unknown
• r.(?) = RNA not analysed but probably transcribed copy of DNA variant
• r.spl? = RNA not analysed but variant probably affects splicing
• r.(spl?) = RNA not analysed but variant may affect splicing
• r.0? = change expected to abolish transcription

Protein: Description of variant at protein level (following HGVS recommendations).

• p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
• p.Arg345Pro = change derived from RNA analysis
• p.? = unknown effect
• p.0? = probably no protein produced

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

• benign = Benign
• possiblyDamaging = Possibly damaging
• probablyDamaging = Probably damaging
• noPrediction = No prediction

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

• intergenic
• near-gene-5
• utr-5
• coding
• coding-near-splice
• coding-synonymous
• coding-synonymous-near-splice
• codingComplex
• codingComplex-near-splice
• frameshift
• frameshift-near-splice
• missense
• missense-near-splice
• splice-5
• intron
• splice-3
• stop-gained
• stop-gained-near-splice
• stop-lost
• stop-lost-near-splice
• utr-3
• near-gene-3

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

3 entries on 1 page. Showing entries 1 - 3.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	RNA change	Protein	PolyPhen	GVS function	Splice distance	SIFT
POLG	00000266	NM_001126131.1	0000017569	./.	-	-	c.3700C>A	-	r.(=)	p.(=)	-	-	-	-
POLG	00000267	NM_002693.2	0000017569	./.	-	-	c.3700C>A	-	r.(=)	p.(=)	-	-	-	-
FANCI	00003110	NM_018193.2	0000017569	./.	-	-	c.*312G>T	-	r.(=)	p.(=)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000292852; RCV000387145; RCV000794915; RCV001121231;
Chromosome	15:89860002..89860002
ClinVar Allele ID	340031
Disease database name and identifier	MedGen:C4763519|MONDO:MONDO:0019391, MeSH:D005199, MedGen:C0015625, OMIM:PS227650, Orphanet:84|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726|MONDO:MONDO:0012186, MedGen:C1836861, OMIM:609053, Orphanet:84
ClinVar preferred disease name	POLG-Related Spectrum Disorders|Fanconi anemia|Progressive sclerosing poliodystrophy|Fanconi anemia complementation group I
HGVS variant names	NC 000015.9:g.89860002G>C
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA10646677
Gene symbol:Gene id.	POLG:5428|FANCI:55215|POLGARF:125316803
Molecular consequence	SO:0001583|missense variant, SO:0001624|3 prime UTR variant
Allele origin	germline
dbSNP ID	144346886
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000127550; RCV000536053; RCV000710187; RCV002345437;
Chromosome	15:89860002..89860002
Allele frequencies from ESP	0.00085
Allele frequencies from TGP	0.00080
ClinVar Allele ID	142470
Disease database name and identifier	MedGen:CN169374|MeSH:D030342, MedGen:C0950123|MedGen:C3661900|MONDO:MONDO:0008758, MedGen:C0205710, OMIM:203700, Orphanet:726
ClinVar preferred disease name	not specified|Inborn genetic diseases|not provided|Progressive sclerosing poliodystrophy
HGVS variant names	NC 000015.9:g.89860002G>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Benign(2)|Likely benign(4)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA292858
Gene symbol:Gene id.	POLG:5428|FANCI:55215|POLGARF:125316803
Molecular consequence	SO:0001624|3 prime UTR variant, SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	144346886
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:

None

Ensembl Variant Phenotype Information:

None