rs3832613

chr9-2014019-G-GTTTTAAchr9-2014019-G-GTTTTAATT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000637383.1(SMARCA2):c.-36-14967_-36-14962dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,670 control chromosomes in the GnomAD database, including 15,354 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15354 hom., cov: 0)
• Consequence: SMARCA2 ENST00000637383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

Genes affected

SMARCA2 (HGNC:11098): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2) The protein encoded by this gene is a member of the SWI/SNF family of proteins and is highly 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, which contains a trinucleotide repeat (CAG) length polymorphism. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCA2	ENST00000637383.1	c.-36-14967_-36-14962dup		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67706 AN: 151552 Hom.: 15326 Cov.: 0

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.447 AC: 67778 AN: 151670 Hom.: 15354 Cov.: 0 AF XY: 0.443 AC XY: 32844 AN XY: 74156

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.409

Alfa AF: 0.425 Hom.: 1474

Asia WGS AF: 0.375 AC: 1308 AN: 3478

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

LitVar

Other links and lift over

dbSNP: rs3832613; hg19: chr9-2014019;