Genetic Variant SMARCA1:p.Arg981Lys (chrX-129465608-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_001282874.2(SMARCA1):c.2942G>A(p.Arg981Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000275 in 1,198,675 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000062 ( 0 hom., 2 hem., cov: 22)

Exomes 𝑓: 0.000024 ( 0 hom. 3 hem. )

Consequence

SMARCA1
NM_001282874.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.08

Variant links:

Genes affected

SMARCA1 (HGNC:11097): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1) This gene encodes a member of the SWI/SNF family of proteins. The encoded protein is an ATPase which is expressed in diverse tissues and contributes to the chromatin remodeling complex that is involved in transcription. The protein may also play a role in DNA damage, growth inhibition and apoptosis of cancer cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

SMARCA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.051436514).

BS2

High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMARCA1	NM_001282874.2 link	c.2942G>A	p.Arg981Lys	missense_variant	Exon 23 of 25	ENST00000371121.5	NP_001269803.1	B7ZLQ5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SMARCA1	ENST00000371121.5 link	c.2942G>A	p.Arg981Lys	missense_variant	Exon 23 of 25	1	NM_001282874.2	ENSP00000360162.4	B7ZLQ5
SMARCA1	ENST00000371123.5 link	c.2906G>A	p.Arg969Lys	missense_variant	Exon 22 of 24	1		ENSP00000360164.2	A0A0A0MRP6
SMARCA1	ENST00000371122.8 link	c.2942G>A	p.Arg981Lys	missense_variant	Exon 23 of 25	1		ENSP00000360163.4	P28370-1
SMARCA1	ENST00000617310.4 link	n.3260G>A		non_coding_transcript_exon_variant	Exon 21 of 23	2

Frequencies

GnomAD3 genomes

AF:

0.0000625

AC:

AN:

111995

Hom.:

Cov.:

AF XY:

0.0000585

AC XY:

AN XY:

34167

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000569

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000660

GnomAD3 exomes

AF:

0.0000386

AC:

AN:

181388

Hom.:

AF XY:

0.00

AC XY:

AN XY:

66088

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000259

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000239

AC:

AN:

1086624

Hom.:

Cov.:

AF XY:

0.00000852

AC XY:

AN XY:

352294

show subpopulations

Gnomad4 AFR exome

AF:

0.0000382

Gnomad4 AMR exome

AF:

0.000399

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:

0.00

Gnomad4 OTH exome

AF:

0.000241

GnomAD4 genome

AF:

0.0000625

AC:

AN:

112051

Hom.:

Cov.:

AF XY:

0.0000584

AC XY:

AN XY:

34233

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000568

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.000651

Alfa

AF:

0.000136

Hom.:

Bravo

AF:

0.000121

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Aug 10, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2942G>A (p.R981K) alteration is located in exon 23 (coding exon 23) of the SMARCA1 gene. This alteration results from a G to A substitution at nucleotide position 2942, causing the arginine (R) at amino acid position 981 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.20

BayesDel_noAF

Benign

-0.24

CADD

Benign

DANN

Benign

0.83

DEOGEN2

Benign

0.013

T;T;.

FATHMM_MKL

Benign

0.72

LIST_S2

Uncertain

0.87

D;T;T

M_CAP

Benign

0.017

MetaRNN

Benign

0.051

T;T;T

MetaSVM

Benign

-0.58

MutationAssessor

Benign

-0.28

N;.;.

PrimateAI

Uncertain

0.79

PROVEAN

Benign

0.71

N;N;N

REVEL

Benign

0.27

Sift

Benign

1.0

T;T;D

Sift4G

Benign

1.0

T;T;T

Polyphen

0.0

B;.;B

Vest4

0.17

MVP

0.85

MPC

0.62

ClinPred

0.098

GERP RS

4.7

Varity_R

0.15

gMVP

0.54

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