Variant chr13-46771452-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_001984.2(ESD):c.813C>T(p.Asp271=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00633 in 1,607,514 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0048 ( 4 hom., cov: 31)

Exomes 𝑓: 0.0065 ( 52 hom. )

Consequence

ESD
NM_001984.2 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.32

Variant links:

Genes affected

ESD (HGNC:3465): (esterase D) This gene encodes a serine hydrolase that belongs to the esterase D family. The encoded enzyme is active toward numerous substrates including O-acetylated sialic acids, and it may be involved in the recycling of sialic acids. This gene is used as a genetic marker for retinoblastoma and Wilson's disease. [provided by RefSeq, Feb 2009]

ESD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 13-46771452-G-A is Benign according to our data. Variant chr13-46771452-G-A is described in ClinVar as [Benign]. Clinvar id is 770992.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.32 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ESD	NM_001984.2 linkuse as main transcript	c.813C>T	p.Asp271=	synonymous_variant	10/10	ENST00000378720.8
ESD	XM_005266278.4 linkuse as main transcript	c.813C>T	p.Asp271=	synonymous_variant	10/10
ESD	XM_011534954.2 linkuse as main transcript	c.813C>T	p.Asp271=	synonymous_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESD	ENST00000378720.8 linkuse as main transcript	c.813C>T	p.Asp271=	synonymous_variant	10/10	1	NM_001984.2	P1
ESD	ENST00000378697.5 linkuse as main transcript	c.726C>T	p.Asp242=	synonymous_variant	11/11	5

Frequencies

GnomAD3 genomes

AF:

0.00476

AC:

722

AN:

151808

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000944

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00525

Gnomad ASJ

AF:

0.0257

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00934

Gnomad FIN

AF:

0.000569

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00665

Gnomad OTH

AF:

0.00336

GnomAD3 exomes

AF:

0.00581

AC:

1452

AN:

249968

Hom.:

AF XY:

0.00641

AC XY:

867

AN XY:

135156

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00349

Gnomad ASJ exome

AF:

0.0269

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00763

Gnomad FIN exome

AF:

0.000651

Gnomad NFE exome

AF:

0.00671

Gnomad OTH exome

AF:

0.00607

GnomAD4 exome

AF:

0.00649

AC:

9449

AN:

1455588

Hom.:

Cov.:

AF XY:

0.00659

AC XY:

4772

AN XY:

724424

show subpopulations

Gnomad4 AFR exome

AF:

0.000840

Gnomad4 AMR exome

AF:

0.00328

Gnomad4 ASJ exome

AF:

0.0249

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00777

Gnomad4 FIN exome

AF:

0.00111

Gnomad4 NFE exome

AF:

0.00679

Gnomad4 OTH exome

AF:

0.00612

GnomAD4 genome

AF:

0.00475

AC:

722

AN:

151926

Hom.:

Cov.:

AF XY:

0.00466

AC XY:

346

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.000941

Gnomad4 AMR

AF:

0.00524

Gnomad4 ASJ

AF:

0.0257

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00934

Gnomad4 FIN

AF:

0.000569

Gnomad4 NFE

AF:

0.00665

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00704

Hom.:

Bravo

AF:

0.00434

Asia WGS

AF:

0.00318

AC:

AN:

3470

EpiCase

AF:

0.00765

EpiControl

AF:

0.00724

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	Labcorp Genetics (formerly Invitae), Labcorp	Aug 08, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

4.2

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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