View genomic variant #0000015840

Variant on transcripts

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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

1 entry on 1 page. Showing entry 1.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	DNA change (cDNA)	Protein	GVS function	Position	Exon	PolyPhen	RNA change	SIFT
RET	00003304	NM_020975.4	0000015840	./.	c.3243T>C	p.(=)	-	-	-	-	r.(=)	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000123320; RCV000410847; RCV000412402; RCV000570968; RCV001103047; RCV001103048; RCV001108244; RCV001108245;
Chromosome	10:43623615..43623615
Allele frequencies from ESP	0.00031
Allele frequencies from ExAC	0.00013
ClinVar Allele ID	139830
Disease database name and identifier	MONDO:MONDO:0017169, MedGen:C0027662, OMIM:PS131100, Orphanet:276161|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MONDO:MONDO:0019003, MedGen:C4048306, Orphanet:653|MONDO:MONDO:0008082, MeSH:D018814, MedGen:C0025269, OMIM:162300, Orphanet:247709, Orphanet:653|MONDO:MONDO:0007723, MedGen:C3888239, OMIM:142623, Orphanet:388|MONDO:MONDO:0008234, MeSH:D018813, MedGen:C0025268, OMIM:171400, Orphanet:247698, Orphanet:653|Human Phenotype Ontology:HP:0002666, MONDO:MONDO:0008233, MedGen:C0031511, OMIM:171300, Orphanet:29072|MONDO:MONDO:0024519, MedGen:C1619700, OMIM:191830, Orphanet:411709
ClinVar preferred disease name	Multiple endocrine neoplasia|Hereditary cancer-predisposing syndrome|Multiple endocrine neoplasia, type 2|Multiple endocrine neoplasia, type 2b|Hirschsprung disease, susceptibility to, 1|Multiple endocrine neoplasia, type 2a|Pheochromocytoma|Renal hypodysplasia/aplasia 1
HGVS variant names	NC 000010.10:g.43623615T>C
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(2)|Benign(2)|Likely benign(4)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA010921
Gene symbol:Gene id.	RET:5979
Molecular consequence	SO:0001819|synonymous variant
Allele origin	germline
dbSNP ID	144192900
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