rs1555753732

Positions:

• chr19-10986541-TGGCCCC-T
• chr19-10986541-TGGCCCC-TGGCCCCGGCCCC

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP6

The NM_003072.5(SMARCA4):​c.714_719delCGGCCC​(p.Gly239_Pro240del) variant causes a disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SMARCA4 NM_003072.5 disruptive_inframe_deletion
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: 6.66

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 19-10986541-TGGCCCC-T is Benign according to our data. Variant chr19-10986541-TGGCCCC-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 643805.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	5/35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	4/34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.714_719delCGGCCC	p.Gly239_Pro240del	disruptive_inframe_deletion	5/35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.126_131delCGGCCC	p.Gly43_Pro44del	disruptive_inframe_deletion	1/32			ENSP00000496004.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Rhabdoid tumor predisposition syndrome 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 11, 2018

This variant, c.714_719delCGGCCC, results in the deletion of 2 amino acids of the SMARCA4 protein (p.Gly243_Pro244del), but otherwise preserves the integrity of the reading frame. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with SMARCA4-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Hereditary cancer-predisposing syndrome Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 24, 2023

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555753732; hg19: chr19-11097217;