Variant 11-65582285-T-G 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_001099409.3(EHBP1L1):c.1613T>G(p.Val538Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,527,610 control chromosomes in the GnomAD database, including 181,234 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.45 ( 16336 hom., cov: 33)

Exomes 𝑓: 0.49 ( 164898 hom. )

Consequence

EHBP1L1
NM_001099409.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.116

Variant links:

Genes affected

EHBP1L1 (HGNC:30682): (EH domain binding protein 1 like 1) Predicted to be involved in actin cytoskeleton organization. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

EHBP1L1 links:

EHBP1L1 (HGNC:):

EHBP1L1 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 (MetaRNN=4.8787624E-5).

BP6

Variant 11-65582285-T-G is Benign according to our data. Variant chr11-65582285-T-G is described in ClinVar as [Benign]. Clinvar id is 1265858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EHBP1L1	NM_001099409.3 linkuse as main transcript	c.1613T>G	p.Val538Gly	missense_variant	9/19	ENST00000309295.9	NP_001092879.1	Q8N3D4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EHBP1L1	ENST00000309295.9 linkuse as main transcript	c.1613T>G	p.Val538Gly	missense_variant	9/19	1	NM_001099409.3	ENSP00000312671.4		Q8N3D4

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68815

AN:

151824

Hom.:

16332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.544

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.453

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.517

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.480

GnomAD3 exomes

AF:

0.475

AC:

80724

AN:

169966

Hom.:

19519

AF XY:

0.484

AC XY:

44130

AN XY:

91128

show subpopulations

Gnomad AFR exome

AF:

0.322

Gnomad AMR exome

AF:

0.351

Gnomad ASJ exome

AF:

0.453

Gnomad EAS exome

AF:

0.464

Gnomad SAS exome

AF:

0.527

Gnomad FIN exome

AF:

0.608

Gnomad NFE exome

AF:

0.497

Gnomad OTH exome

AF:

0.494

GnomAD4 exome

AF:

0.487

AC:

670315

AN:

1375666

Hom.:

164898

Cov.:

AF XY:

0.489

AC XY:

331097

AN XY:

676658

show subpopulations

Gnomad4 AFR exome

AF:

0.322

Gnomad4 AMR exome

AF:

0.357

Gnomad4 ASJ exome

AF:

0.454

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.600

Gnomad4 NFE exome

AF:

0.491

Gnomad4 OTH exome

AF:

0.466

GnomAD4 genome

AF:

0.453

AC:

68848

AN:

151944

Hom.:

16336

Cov.:

AF XY:

0.459

AC XY:

34079

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.453

Gnomad4 EAS

AF:

0.466

Gnomad4 SAS

AF:

0.516

Gnomad4 FIN

AF:

0.619

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.484

Alfa

AF:

0.484

Hom.:

30128

Bravo

AF:

0.426

TwinsUK

AF:

0.487

AC:

1805

ALSPAC

AF:

0.496

AC:

1910

ESP6500AA

AF:

0.315

AC:

1180

ESP6500EA

AF:

0.474

AC:

3862

ExAC

AF:

0.458

AC:

53907

Asia WGS

AF:

0.469

AC:

1631

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	Apr 27, 2020	This variant is associated with the following publications: (PMID: 20708005) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.072

Eigen

Uncertain

0.21

Eigen_PC

Benign

0.22

FATHMM_MKL

Uncertain

0.80

LIST_S2

Benign

0.27

MetaRNN

Benign

0.000049

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.1

PrimateAI

Benign

0.34

PROVEAN

Uncertain

-3.0

REVEL

Benign

0.25

Sift

Benign

0.095

Sift4G

Benign

0.21

Polyphen

0.96

Vest4

0.078

MPC

0.051

ClinPred

0.025

GERP RS

3.8

Varity_R

0.28

gMVP

0.35

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