View genomic variant #0000019622

Variant on transcripts

Legend

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

2 entries on 1 page. Showing entries 1 - 2.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Position	RNA change	Protein	PolyPhen	GVS function	Splice distance	SIFT
BCS1L	00000013	NM_001079866.1	0000019622	./.	-	-	c.889+1G>T	-	r.spl?	p.?	-	-	-	-
BCS1L	00000012	NM_004328.4	0000019622	./.	-	-	c.889+1G>T	-	r.spl?	p.?	-	-	-	-

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000669828;
Chromosome	2:219527403..219527404
ClinVar Allele ID	541905
Disease database name and identifier	MONDO:MONDO:0011308, MedGen:C1864002, OMIM:603358, Orphanet:53693
ClinVar preferred disease name	GRACILE syndrome
HGVS variant names	NC 000002.11:g.219527404dup
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	BCS1L:617
Molecular consequence	SO:0001575|splice donor variant
Allele origin	unknown
dbSNP ID	1553597661
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000411192; RCV000522697; RCV002502421; RCV003475942;
Chromosome	2:219527403..219527403
ClinVar Allele ID	357243
Disease database name and identifier	MedGen:C3661900|MONDO:MONDO:0011308, MedGen:C1864002, OMIM:603358, Orphanet:53693|MONDO:MONDO:0007415, MedGen:C3541471, OMIM:124000, Orphanet:254902|MONDO:MONDO:0009872, MedGen:C0266006, OMIM:262000, Orphanet:123
ClinVar preferred disease name	not provided|GRACILE syndrome|Mitochondrial complex III deficiency nuclear type 1|Pili torti-deafness syndrome
HGVS variant names	NC 000002.11:g.219527403G>T
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA16040864
Gene symbol:Gene id.	BCS1L:617
Molecular consequence	SO:0001575|splice donor variant
Allele origin	germline
dbSNP ID	1057516346
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