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NM_003073.5(SMARCB1):c.607G>A (p.Ala203Thr) AND Rhabdoid tumor predisposition syndrome 2

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 8, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001789772.3

Allele description [Variation Report for NM_003073.5(SMARCB1):c.607G>A (p.Ala203Thr)]

NM_003073.5(SMARCB1):c.607G>A (p.Ala203Thr)

Gene:
SMARCB1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q11.23
Genomic location:
Preferred name:
NM_003073.5(SMARCB1):c.607G>A (p.Ala203Thr)
HGVS:
  • NC_000022.11:g.23803401G>A
  • NG_009303.1:g.21439G>A
  • NM_001007468.3:c.580G>A
  • NM_001317946.2:c.634G>A
  • NM_001362877.2:c.661G>A
  • NM_003073.5:c.607G>AMANE SELECT
  • NP_001007469.1:p.Ala194Thr
  • NP_001304875.1:p.Ala212Thr
  • NP_001349806.1:p.Ala221Thr
  • NP_003064.2:p.Ala203Thr
  • LRG_520t1:c.607G>A
  • LRG_520:g.21439G>A
  • NC_000022.10:g.24145588G>A
  • NM_003073.3:c.607G>A
  • NM_003073.4:c.607G>A
Protein change:
A194T
Links:
dbSNP: rs762962010
NCBI 1000 Genomes Browser:
rs762962010
Molecular consequence:
  • NM_001007468.3:c.580G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317946.2:c.634G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362877.2:c.661G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003073.5:c.607G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Rhabdoid tumor predisposition syndrome 2 (RTPS2)
Identifiers:
MONDO: MONDO:0013224; MedGen: C2750074; Orphanet: 231108; Orphanet: 69077; OMIM: 613325

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002032305St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Dec 8, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002032305.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The SMARCB1 c.607G>A (p.Ala203Thr) missense change has a maximum subpopulation frequency of 0.0035% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/22-24145588-G-A?dataset=gnomad_r2_1). Four of six in silico tools predict a benign effect of this variant on protein function (BP4), but to our knowledge these predictions have not been confirmed by functional assays. This variant occurs in a gene where missense variants are more likely to be damaging based on methods described by Lek et al. (PP2; PMID: 27535533). To our knowledge, this variant has not been reported in individuals with rhabdoid tumor predisposition syndrome. In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: BP4, PP2.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024