Variant chr11-76546171-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001300942.2(EMSY):c.3693T>C(p.Thr1231=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 1,613,946 control chromosomes in the GnomAD database, including 74,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 5842 hom., cov: 32)

Exomes 𝑓: 0.30 ( 68731 hom. )

Consequence

EMSY
NM_001300942.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.884

Variant links:

Genes affected

EMSY (HGNC:18071): (EMSY transcriptional repressor, BRCA2 interacting) Predicted to enable identical protein binding activity. Predicted to be involved in DNA repair; chromatin organization; and regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

EMSY links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 11-76546171-T-C is Benign according to our data. Variant chr11-76546171-T-C is described in ClinVar as [Benign]. Clinvar id is 3060664.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.884 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EMSY	NM_001300942.2 linkuse as main transcript	c.3693T>C	p.Thr1231=	synonymous_variant	21/22	ENST00000695367.1	NP_001287871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMSY	ENST00000695367.1 linkuse as main transcript	c.3693T>C	p.Thr1231=	synonymous_variant	21/22		NM_001300942.2	ENSP00000511840		Q7Z589-7

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

41053

AN:

152010

Hom.:

5838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.267

AC:

67132

AN:

251174

Hom.:

9915

AF XY:

0.271

AC XY:

36830

AN XY:

135734

show subpopulations

Gnomad AFR exome

AF:

0.209

Gnomad AMR exome

AF:

0.153

Gnomad ASJ exome

AF:

0.389

Gnomad EAS exome

AF:

0.122

Gnomad SAS exome

AF:

0.239

Gnomad FIN exome

AF:

0.326

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.302

AC:

441176

AN:

1461818

Hom.:

68731

Cov.:

AF XY:

0.301

AC XY:

219014

AN XY:

727200

show subpopulations

Gnomad4 AFR exome

AF:

0.203

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.138

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.326

Gnomad4 NFE exome

AF:

0.318

Gnomad4 OTH exome

AF:

0.294

GnomAD4 genome

AF:

0.270

AC:

41060

AN:

152128

Hom.:

5842

Cov.:

AF XY:

0.269

AC XY:

19993

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.338

Gnomad4 NFE

AF:

0.316

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.302

Hom.:

4935

Bravo

AF:

0.259

Asia WGS

AF:

0.189

AC:

658

AN:

3478

EpiCase

AF:

0.318

EpiControl

AF:

0.312

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

EMSY-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 27, 2021

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

6.4

DANN

Benign

0.63

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