rs3832613

Variant names:

• chr9-2014019-G-GTTTTAA
• rs3832613
• ENST00000637383.1:c.-36-14968_-36-14967insTTTTAA

Your query was ambiguous. Multiple possible variants found:

• chr9-2014019-G-GTTTTAA
• chr9-2014019-G-GTTTTAATT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000637383.1(SMARCA2):​c.-36-14968_-36-14967insTTTTAA variant causes a intron change involving the alteration of a non-conserved nucleotide. 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
• Publications: 4 publications found

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]

SMARCA2 Gene-Disease associations (from GenCC):

• intellectual disability-sparse hair-brachydactyly syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• blepharophimosis-impaired intellectual development syndrome

  Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637383.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMARCA2	ENST00000637383.1	TSL:5	c.-36-14968_-36-14967insTTTTAA		intron	N/A	ENSP00000489645.1	A0A1B0GTC9

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

African (AFR) AF: 0.512 AC: 21142 AN: 41286

American (AMR) AF: 0.435 AC: 6641 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1622 AN: 3456

East Asian (EAS) AF: 0.297 AC: 1541 AN: 5180

South Asian (SAS) AF: 0.412 AC: 1983 AN: 4810

European-Finnish (FIN) AF: 0.377 AC: 3968 AN: 10534

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29615 AN: 67836

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.425 Hom.: 1474

Asia WGS AF: 0.375 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs3832613; hg19: chr9-2014019;