rs876657378

Variant names:

• chr19-10996249-CAGA-C
• rs876657378
• NM_001387283.1:c.1636_1638delAAG

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PM4_Supporting PP5_Moderate

The NM_003072.5(SMARCA4):​c.1636_1638delAAG​(p.Lys546del) variant causes a conservative inframe deletion 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 (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SMARCA4 NM_003072.5 conservative_inframe_deletion
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 9.23

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 Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_003072.5. Strenght limited to Supporting due to length of the change: 1aa.
• PP5: Variant 19-10996249-CAGA-C is Pathogenic according to our data. Variant chr19-10996249-CAGA-C is described in ClinVar as [Pathogenic]. Clinvar id is 30342.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-10996249-CAGA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 11 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 10 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.1636_1638delAAG	p.Lys546del	conservative_inframe_deletion	Exon 11 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.1048_1050delAAG	p.Lys350del	conservative_inframe_deletion	Exon 7 of 32			ENSP00000496004.1
SMARCA4	ENST00000644963.1	c.280_282delAAG	p.Lys94del	conservative_inframe_deletion	Exon 3 of 28			ENSP00000495599.1
SMARCA4	ENST00000644065.1	c.364_366delAAG	p.Lys122del	conservative_inframe_deletion	Exon 3 of 27			ENSP00000493615.1
SMARCA4	ENST00000642350.1	c.124_126delAAG	p.Lys42del	conservative_inframe_deletion	Exon 2 of 27			ENSP00000495355.1
SMARCA4	ENST00000643857.1	c.-17_-15delAGA		upstream_gene_variant				ENSP00000494159.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual disability, autosomal dominant 16 Pathogenic:1

Mar 18, 2012

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Jun 20, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed in large population cohorts (gnomAD); In-frame deletion of 1 amino acid in a non-repeat region; This variant is associated with the following publications: (PMID: 25168959, 23815551, 23010866, 24700502, 24090879, 23637025, 22426308) -

Computational scores

Source: dbNSFP v4.3

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: rs876657378; hg19: chr19-11106925;