rs372601826

Variant names:

• chr19-10986523-CGGCCCTGGCCCTGGCCCT-C
• NM_001387283.1:c.696_713delTGGCCCTGGCCCTGGCCC

Your query was ambiguous. Multiple possible variants found:

• chr19-10986523-CGGCCCTGGCCCTGGCCCT-C
• chr19-10986523-CGGCCCTGGCCCTGGCCCT-CGGCCCT
• chr19-10986523-CGGCCCTGGCCCTGGCCCT-CGGCCCTGGCCCT
• chr19-10986523-CGGCCCTGGCCCTGGCCCT-CGGCCCTGGCCCTGGCCCTGGCCCT
• chr19-10986523-CGGCCCTGGCCCTGGCCCT-CGGCCCTGGCCCTGGCCCTGGCCCTGGCCCT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003072.5(SMARCA4):​c.696_713delTGGCCCTGGCCCTGGCCC​(p.Gly233_Pro238del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000000719 in 1,391,208 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P232P) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: SMARCA4 NM_003072.5 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.83

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA4	NM_001387283.1	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 36	ENST00000646693.2	NP_001374212.1
SMARCA4	NM_003072.5	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 35	ENST00000344626.10	NP_003063.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMARCA4	ENST00000646693.2	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 36		NM_001387283.1	ENSP00000495368.1
SMARCA4	ENST00000344626.10	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 35	1	NM_003072.5	ENSP00000343896.4
SMARCA4	ENST00000643549.1	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 35			ENSP00000493975.1
SMARCA4	ENST00000541122.6	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 5 of 35	5		ENSP00000445036.2
SMARCA4	ENST00000643296.1	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 34			ENSP00000496635.1
SMARCA4	ENST00000644737.1	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 4 of 34			ENSP00000495548.1
SMARCA4	ENST00000589677.5	c.696_713delTGGCCCTGGCCCTGGCCC	p.Gly233_Pro238del	disruptive_inframe_deletion	Exon 5 of 35	5		ENSP00000464778.1
SMARCA4	ENST00000643995.1	c.108_125delTGGCCCTGGCCCTGGCCC	p.Gly37_Pro42del	disruptive_inframe_deletion	Exon 1 of 32			ENSP00000496004.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.19e-7 AC: 1 AN: 1391208 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 686496

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.27e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-11097199;