Variant chr9-2076174-A-T 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.1936-55A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 968,268 control chromosomes in the GnomAD database, including 5,956 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.094 ( 800 hom., cov: 32)

Exomes 𝑓: 0.10 ( 5156 hom. )

Consequence

SMARCA2
NM_003070.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.619

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:

SMARCA2 (HGNC:):

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=-0.81).

BP6

Variant 9-2076174-A-T is Benign according to our data. Variant chr9-2076174-A-T is described in ClinVar as [Benign]. Clinvar id is 1270525.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SMARCA2	NM_003070.5 linkuse as main transcript	c.1936-55A>T	intron_variant	ENST00000349721.8	NP_003061.3	P51531-1Q8N9Q1Q56A76
SMARCA2	NM_001289396.1 linkuse as main transcript	c.1936-55A>T	intron_variant		NP_001276325.1	P51531-1Q8N9Q1B4DSC8
SMARCA2	NM_139045.4 linkuse as main transcript	c.1936-55A>T	intron_variant		NP_620614.2	P51531-2Q8N9Q1Q56A76
SMARCA2	NM_001289397.2 linkuse as main transcript	c.1936-55A>T	intron_variant		NP_001276326.1	P51531F6VDE0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCA2	ENST00000349721.8 linkuse as main transcript	c.1936-55A>T		intron_variant		5	NM_003070.5	ENSP00000265773.5		P51531-1

Frequencies

GnomAD3 genomes

AF:

0.0937

AC:

14250

AN:

152078

Hom.:

795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0582

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.103

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0874

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.103

AC:

83770

AN:

816072

Hom.:

5156

AF XY:

0.101

AC XY:

43498

AN XY:

431776

show subpopulations

Gnomad4 AFR exome

AF:

0.0591

Gnomad4 AMR exome

AF:

0.179

Gnomad4 ASJ exome

AF:

0.0922

Gnomad4 EAS exome

AF:

0.267

Gnomad4 SAS exome

AF:

0.0975

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.0886

Gnomad4 OTH exome

AF:

0.105

GnomAD4 genome

AF:

0.0938

AC:

14272

AN:

152196

Hom.:

800

Cov.:

AF XY:

0.0968

AC XY:

7206

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.0581

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.103

Gnomad4 EAS

AF:

0.276

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.0874

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.0289

Hom.:

Bravo

AF:

0.0966

Asia WGS

AF:

0.229

AC:

794

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 08, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.35

DANN

Benign

0.76

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