Variant rs3812619 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.134G>A(p.Arg45Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.096 in 1,613,782 control chromosomes in the GnomAD database, including 12,414 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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 0.16 ( 3139 hom., cov: 32)

Exomes 𝑓: 0.090 ( 9275 hom. )

Consequence

ECD
NM_007265.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.12

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:

ECD (HGNC:):

ECD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035088956).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ECD	NM_007265.3 linkuse as main transcript	c.134G>A	p.Arg45Gln	missense_variant	2/14	ENST00000372979.9	NP_009196.1	O95905-1
ECD	NM_001135752.1 linkuse as main transcript	c.134G>A	p.Arg45Gln	missense_variant	2/15		NP_001129224.1	O95905-3
ECD	NM_001135753.1 linkuse as main transcript	c.134G>A	p.Arg45Gln	missense_variant	2/13		NP_001129225.1	O95905-2
ECD	NR_024203.1 linkuse as main transcript	n.231-3253G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ECD	ENST00000372979.9 linkuse as main transcript	c.134G>A	p.Arg45Gln	missense_variant	2/14	1	NM_007265.3	ENSP00000362070.4		O95905-1

Frequencies

GnomAD3 genomes

AF:

0.157

AC:

23873

AN:

151888

Hom.:

3114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.335

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.106

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.0423

Gnomad MID

AF:

0.0764

Gnomad NFE

AF:

0.0653

Gnomad OTH

AF:

0.126

GnomAD3 exomes

AF:

0.126

AC:

31788

AN:

251458

Hom.:

3257

AF XY:

0.126

AC XY:

17109

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.0945

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.306

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.0459

Gnomad NFE exome

AF:

0.0658

Gnomad OTH exome

AF:

0.0938

GnomAD4 exome

AF:

0.0896

AC:

131028

AN:

1461774

Hom.:

9275

Cov.:

AF XY:

0.0927

AC XY:

67407

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.346

Gnomad4 AMR exome

AF:

0.0959

Gnomad4 ASJ exome

AF:

0.124

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.0472

Gnomad4 NFE exome

AF:

0.0645

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.158

AC:

23950

AN:

152008

Hom.:

3139

Cov.:

AF XY:

0.158

AC XY:

11745

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.336

Gnomad4 AMR

AF:

0.106

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.306

Gnomad4 SAS

AF:

0.232

Gnomad4 FIN

AF:

0.0423

Gnomad4 NFE

AF:

0.0654

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.0911

Hom.:

2543

Bravo

AF:

0.168

TwinsUK

AF:

0.0583

AC:

216

ALSPAC

AF:

0.0615

AC:

237

ESP6500AA

AF:

0.325

AC:

1433

ESP6500EA

AF:

0.0717

AC:

617

ExAC

AF:

0.134

AC:

16203

Asia WGS

AF:

0.270

AC:

937

AN:

3478

EpiCase

AF:

0.0657

EpiControl

AF:

0.0653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.066

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.56

DEOGEN2

Benign

0.018

T;.;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-0.98

FATHMM_MKL

Benign

0.038

LIST_S2

Benign

0.21

T;T;T;T

MetaRNN

Benign

0.0035

T;T;T;T

MetaSVM

Benign

-0.89

PrimateAI

Benign

0.23

PROVEAN

Benign

0.57

N;N;N;N

REVEL

Benign

0.029

Sift

Benign

0.98

T;T;T;T

Sift4G

Benign

0.59

T;T;T;T

Polyphen

0.0

B;.;.;.

Vest4

0.052

MPC

0.092

ClinPred

0.0023

GERP RS

3.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.014

gMVP

0.19

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