View genomic variant #0000015673

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.

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.

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

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

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

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.

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

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

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

SIFT: SIFT Annotation

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

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
USH2A	00003116	NM_007123.5	0000015673	./.	c.3801G>A	p.(=)	-	-	-	-	r.(=)	-
USH2A	00003348	NM_206933.2	0000015673	./.	c.3801G>A	p.(=)	-	-	-	-	r.(=)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000152619; RCV000295631; RCV000389900; RCV001075377; RCV001207755;
Chromosome	1:216372979..216372979
Allele frequencies from ExAC	0.00004
Allele frequencies from TGP	0.00040
ClinVar Allele ID	172911
Disease database name and identifier	Human Phenotype Ontology:HP:0000556, Human Phenotype Ontology:HP:0007736, Human Phenotype Ontology:HP:0007910, Human Phenotype Ontology:HP:0007974, Human Phenotype Ontology:HP:0007982, MONDO:MONDO:0019118, MeSH:D058499, MedGen:C0854723, Orphanet:71862|MONDO:MONDO:0010169, MedGen:C1848634, OMIM:276901, Orphanet:231178, Orphanet:886|Human Phenotype Ontology:HP:0000547, MONDO:MONDO:0019200, MeSH:D012174, MedGen:C0035334, OMIM:268000, OMIM:PS268000, Orphanet:791|MedGen:CN169374|MedGen:C3661900
ClinVar preferred disease name	Retinal dystrophy|Usher syndrome type 2A|Retinitis pigmentosa|not specified|not provided
HGVS variant names	NC 000001.10:g.216372979C>T
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(3)|Likely benign(3)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA179570
Gene symbol:Gene id.	USH2A:7399|USH2A-AS1:105372918
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	537863698
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