Variant rs2271904 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007265.3(ECD):c.1901A>G(p.Asp634Gly) variant causes a missense change. The variant allele was found at a frequency of 0.083 in 1,614,064 control chromosomes in the GnomAD database, including 8,384 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.10 ( 1238 hom., cov: 32)

Exomes 𝑓: 0.081 ( 7146 hom. )

Consequence

ECD
NM_007265.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.68

Variant links:

Genes affected

ECD (HGNC:17029): (ecdysoneless cell cycle regulator) Enables histone acetyltransferase binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ECD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017505586).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ECD	NM_007265.3 linkuse as main transcript	c.1901A>G	p.Asp634Gly	missense_variant	14/14	ENST00000372979.9
ECD	NM_001135752.1 linkuse as main transcript	c.2000A>G	p.Asp667Gly	missense_variant	15/15
ECD	NM_001135753.1 linkuse as main transcript	c.1772A>G	p.Asp591Gly	missense_variant	13/13
ECD	NR_024203.1 linkuse as main transcript	n.1733A>G		non_coding_transcript_exon_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECD	ENST00000372979.9 linkuse as main transcript	c.1901A>G	p.Asp634Gly	missense_variant	14/14	1	NM_007265.3	P1	O95905-1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15923

AN:

152140

Hom.:

1218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0882

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.0411

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0607

Gnomad OTH

AF:

0.0938

GnomAD3 exomes

AF:

0.110

AC:

27648

AN:

251416

Hom.:

2389

AF XY:

0.113

AC XY:

15338

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.161

Gnomad AMR exome

AF:

0.0857

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.306

Gnomad SAS exome

AF:

0.226

Gnomad FIN exome

AF:

0.0437

Gnomad NFE exome

AF:

0.0609

Gnomad OTH exome

AF:

0.0851

GnomAD4 exome

AF:

0.0807

AC:

117965

AN:

1461806

Hom.:

7146

Cov.:

AF XY:

0.0846

AC XY:

61522

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.0867

Gnomad4 ASJ exome

AF:

0.111

Gnomad4 EAS exome

AF:

0.280

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.0451

Gnomad4 NFE exome

AF:

0.0602

Gnomad4 OTH exome

AF:

0.0934

GnomAD4 genome

AF:

0.105

AC:

15983

AN:

152258

Hom.:

1238

Cov.:

AF XY:

0.107

AC XY:

7985

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.0882

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.304

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.0411

Gnomad4 NFE

AF:

0.0608

Gnomad4 OTH

AF:

0.0961

Alfa

AF:

0.0769

Hom.:

1549

Bravo

AF:

0.108

TwinsUK

AF:

0.0550

AC:

204

ALSPAC

AF:

0.0579

AC:

223

ESP6500AA

AF:

0.151

AC:

665

ESP6500EA

AF:

0.0664

AC:

571

ExAC

AF:

0.114

AC:

13818

Asia WGS

AF:

0.259

AC:

898

AN:

3478

EpiCase

AF:

0.0610

EpiControl

AF:

0.0600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.34

T;.;.

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.56

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.85

T;T;T

MetaRNN

Benign

0.0018

T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.9e-7

P;P;P

PrimateAI

Benign

0.41

PROVEAN

Pathogenic

-4.4

D;D;D

REVEL

Benign

0.19

Sift

Uncertain

0.0040

D;D;D

Sift4G

Uncertain

0.0070

D;D;D

Polyphen

0.99

D;.;.

Vest4

0.27

MPC

0.47

ClinPred

0.011

GERP RS

5.7

Varity_R

0.55

gMVP

0.47

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over