rs797045980

Positions:

• chr19-11023577-GC-G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_003072.5(SMARCA4):​c.2922delC​(p.Phe975fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_003072.5 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 7.71

Genes affected

SMARCA4 (HGNC:11100): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

SMARCA4 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-11023577-GC-G is Pathogenic according to our data. Variant chr19-11023577-GC-G is described in ClinVar as [Pathogenic]. Clinvar id is 212245.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.2922delC	p.Phe975fs	frameshift_variant	20/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.2922delC	p.Phe975fs	frameshift_variant	20/35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.2922delC	p.Phe975fs	frameshift_variant	20/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.2922delC	p.Phe975fs	frameshift_variant	20/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.2922delC	p.Phe975fs	frameshift_variant	20/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.2922delC	p.Phe975fs	frameshift_variant	21/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.2922delC	p.Phe975fs	frameshift_variant	20/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.2922delC	p.Phe975fs	frameshift_variant	20/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.2922delC	p.Phe975fs	frameshift_variant	21/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.2334delC	p.Phe779fs	frameshift_variant	17/32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.1566delC	p.Phe523fs	frameshift_variant	13/28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.1647delC	p.Phe550fs	frameshift_variant	13/27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.1407delC	p.Phe470fs	frameshift_variant	12/27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.1275delC	p.Phe426fs	frameshift_variant	11/25			ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 08, 2023	This sequence change creates a premature translational stop signal (p.Phe975Serfs*44) in the SMARCA4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SMARCA4 are known to be pathogenic (PMID: 24658001, 24658002). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SMARCA4-related conditions. ClinVar contains an entry for this variant (Variation ID: 212245). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 21, 2014	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs797045980; hg19: chr19-11134253;