Variant 9-2032845-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003070.5(SMARCA2):c.226-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 974,010 control chromosomes in the GnomAD database, including 22,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4252 hom., cov: 32)

Exomes 𝑓: 0.20 ( 18070 hom. )

Consequence

SMARCA2
NM_003070.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.372

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 9-2032845-G-A is Benign according to our data. Variant chr9-2032845-G-A is described in ClinVar as [Benign]. Clinvar id is 1235432.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SMARCA2	NM_003070.5 linkuse as main transcript	c.226-107G>A	intron_variant	ENST00000349721.8
SMARCA2	NM_001289396.1 linkuse as main transcript	c.226-107G>A	intron_variant
SMARCA2	NM_001289397.2 linkuse as main transcript	c.226-107G>A	intron_variant
SMARCA2	NM_139045.4 linkuse as main transcript	c.226-107G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCA2	ENST00000349721.8 linkuse as main transcript	c.226-107G>A		intron_variant		5	NM_003070.5	P2	P51531-1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34791

AN:

151992

Hom.:

4233

Cov.:

show subpopulations

Gnomad AFR

AF:

0.279

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.309

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.218

GnomAD4 exome

AF:

0.204

AC:

167310

AN:

821900

Hom.:

18070

AF XY:

0.200

AC XY:

84187

AN XY:

420880

show subpopulations

Gnomad4 AFR exome

AF:

0.282

Gnomad4 AMR exome

AF:

0.331

Gnomad4 ASJ exome

AF:

0.150

Gnomad4 EAS exome

AF:

0.335

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.214

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.201

GnomAD4 genome

AF:

0.229

AC:

34846

AN:

152110

Hom.:

4252

Cov.:

AF XY:

0.232

AC XY:

17270

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.279

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.308

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.186

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.181

Hom.:

1504

Bravo

AF:

0.238

Asia WGS

AF:

0.287

AC:

999

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.1

DANN

Benign

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over