Variant 4-143521452-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_003601.4(SMARCA5):c.276C>T(p.Phe92=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00541 in 1,606,132 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0055 ( 34 hom. )

Consequence

SMARCA5
NM_003601.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.22

Variant links:

Genes affected

SMARCA5 (HGNC:11101): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) The protein encoded by this gene is a member of the SWI/SNF family of proteins. 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 protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. [provided by RefSeq, Jul 2008]

SMARCA5 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 (BayesDel_noAF=-0.32).

BP6

Variant 4-143521452-C-T is Benign according to our data. Variant chr4-143521452-C-T is described in ClinVar as [Benign]. Clinvar id is 773457.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 716 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMARCA5	NM_003601.4 linkuse as main transcript	c.276C>T	p.Phe92=	synonymous_variant	3/24	ENST00000283131.4
SMARCA5	XM_047416323.1 linkuse as main transcript	c.276C>T	p.Phe92=	synonymous_variant	3/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMARCA5	ENST00000283131.4 linkuse as main transcript	c.276C>T	p.Phe92=	synonymous_variant	3/24	1	NM_003601.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00474

AC:

715

AN:

150750

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00122

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00271

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00146

Gnomad FIN

AF:

0.0218

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00576

Gnomad OTH

AF:

0.00145

GnomAD3 exomes

AF:

0.00545

AC:

1351

AN:

247866

Hom.:

AF XY:

0.00555

AC XY:

744

AN XY:

133972

show subpopulations

Gnomad AFR exome

AF:

0.00106

Gnomad AMR exome

AF:

0.00204

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00279

Gnomad FIN exome

AF:

0.0216

Gnomad NFE exome

AF:

0.00609

Gnomad OTH exome

AF:

0.00497

GnomAD4 exome

AF:

0.00548

AC:

7980

AN:

1455272

Hom.:

Cov.:

AF XY:

0.00539

AC XY:

3899

AN XY:

723740

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00208

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00313

Gnomad4 FIN exome

AF:

0.0192

Gnomad4 NFE exome

AF:

0.00567

Gnomad4 OTH exome

AF:

0.00451

GnomAD4 genome

AF:

0.00475

AC:

716

AN:

150860

Hom.:

Cov.:

AF XY:

0.00533

AC XY:

392

AN XY:

73552

show subpopulations

Gnomad4 AFR

AF:

0.00122

Gnomad4 AMR

AF:

0.00271

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00167

Gnomad4 FIN

AF:

0.0218

Gnomad4 NFE

AF:

0.00576

Gnomad4 OTH

AF:

0.00143

Alfa

AF:

0.00457

Hom.:

Bravo

AF:

0.00320

Asia WGS

AF:

0.000289

AC:

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

Invitae

Jun 13, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.74

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