Variant 17-40628675-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_003079.5(SMARCE1):c.*110C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 783,098 control chromosomes in the GnomAD database, including 13,353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3944 hom., cov: 33)

Exomes 𝑓: 0.15 ( 9409 hom. )

Consequence

SMARCE1
NM_003079.5 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.199

Variant links:

Genes affected

SMARCE1 (HGNC:11109): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1) The protein encoded by this gene is part of the large ATP-dependent chromatin remodeling complex SWI/SNF, which is required for transcriptional activation of genes normally repressed by chromatin. The encoded protein, either alone or when in the SWI/SNF complex, can bind to 4-way junction DNA, which is thought to mimic the topology of DNA as it enters or exits the nucleosome. The protein contains a DNA-binding HMG domain, but disruption of this domain does not abolish the DNA-binding or nucleosome-displacement activities of the SWI/SNF complex. Unlike most of the SWI/SNF complex proteins, this protein has no yeast counterpart. [provided by RefSeq, Jul 2008]

SMARCE1 links:

SMARCE1 (HGNC:):

SMARCE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 17-40628675-G-A is Benign according to our data. Variant chr17-40628675-G-A is described in ClinVar as [Benign]. Clinvar id is 1230941.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMARCE1	NM_003079.5 linkuse as main transcript	c.*110C>T		3_prime_UTR_variant	11/11	ENST00000348513.12	NP_003070.3	Q969G3-1A0A024R1S7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMARCE1	ENST00000348513 linkuse as main transcript	c.*110C>T		3_prime_UTR_variant	11/11	1	NM_003079.5	ENSP00000323967.6		Q969G3-1

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30693

AN:

152030

Hom.:

3918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.0755

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.169

GnomAD4 exome

AF:

0.147

AC:

92568

AN:

630950

Hom.:

9409

Cov.:

AF XY:

0.143

AC XY:

47604

AN XY:

332202

show subpopulations

Gnomad4 AFR exome

AF:

0.310

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.0689

Gnomad4 EAS exome

AF:

0.292

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.158

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.149

GnomAD4 genome

AF:

0.202

AC:

30778

AN:

152148

Hom.:

3944

Cov.:

AF XY:

0.207

AC XY:

15363

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.316

Gnomad4 ASJ

AF:

0.0755

Gnomad4 EAS

AF:

0.350

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.172

Alfa

AF:

0.129

Hom.:

2250

Bravo

AF:

0.222

Asia WGS

AF:

0.262

AC:

908

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.0

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