19-11059777-C-T

Variant names:

• chr19-11059777-C-T
• rs1555795884
• NM_001387283.1:c.4756C>T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_003072.5(SMARCA4):​c.4660C>T​(p.Gln1554*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 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 stop_gained
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.83

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 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 19-11059777-C-T is Pathogenic according to our data. Variant chr19-11059777-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 537813.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.4756C>T	p.Gln1586*	stop_gained	Exon 34 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.4660C>T	p.Gln1554*	stop_gained	Exon 33 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.4756C>T	p.Gln1586*	stop_gained	Exon 34 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.4660C>T	p.Gln1554*	stop_gained	Exon 33 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.4666C>T	p.Gln1556*	stop_gained	Exon 33 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.4570C>T	p.Gln1524*	stop_gained	Exon 33 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.4570C>T	p.Gln1524*	stop_gained	Exon 32 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.4570C>T	p.Gln1524*	stop_gained	Exon 32 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.4567C>T	p.Gln1523*	stop_gained	Exon 33 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.4081C>T	p.Gln1361*	stop_gained	Exon 30 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.3310C>T	p.Gln1104*	stop_gained	Exon 26 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.3292C>T	p.Gln1098*	stop_gained	Exon 25 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.3154C>T	p.Gln1052*	stop_gained	Exon 25 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.2920C>T	p.Gln974*	stop_gained	Exon 23 of 25			ENSP00000494159.1
SMARCA4	ENST00000538456.4	c.724C>T	p.Gln242*	stop_gained	Exon 6 of 8	3		ENSP00000495197.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Pathogenic:1

May 06, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Gln1586*) 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: 537813). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.65
CADD	Pathogenic	44
DANN	Uncertain	1.0
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.93	D
Vest4		0.98
GERP RS		4.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1555795884; hg19: chr19-11170453; COSMIC: COSV60800247; COSMIC: COSV60800247;