rs17411795

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001142800.2(EYS):c.1922A>T(p.Glu641Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,551,002 control chromosomes in the GnomAD database, including 31,981 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. E641E) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.16 ( 2384 hom., cov: 33)

Exomes 𝑓: 0.20 ( 29597 hom. )

Consequence

EYS
NM_001142800.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.425

Variant links:

Genes affected

EYS (HGNC:21555): (eyes shut homolog) The product of this gene contains multiple epidermal growth factor (EGF)-like and LamG domains. The protein is expressed in the photoreceptor layer of the retina, and the gene is mutated in autosomal recessive retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

EYS 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=0.004574895).

BP6

Variant 6-65295964-T-A is Benign according to our data. Variant chr6-65295964-T-A is described in ClinVar as [Benign]. Clinvar id is 137268.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-65295964-T-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EYS	NM_001142800.2 linkuse as main transcript	c.1922A>T	p.Glu641Val	missense_variant	12/43	ENST00000503581.6
EYS	NM_001292009.2 linkuse as main transcript	c.1922A>T	p.Glu641Val	missense_variant	12/44

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.1922A>T	p.Glu641Val	missense_variant	12/43	5	NM_001142800.2	A2	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.1922A>T	p.Glu641Val	missense_variant	12/44	1		P2	Q5T1H1-3
EYS	ENST00000370615.3 linkuse as main transcript	n.360A>T		non_coding_transcript_exon_variant	2/2	3
EYS	ENST00000447127.1 linkuse as main transcript	n.378A>T		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24611

AN:

151796

Hom.:

2385

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0749

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.0583

Gnomad SAS

AF:

0.0884

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.142

GnomAD3 exomes

AF:

0.168

AC:

26497

AN:

157354

Hom.:

2688

AF XY:

0.165

AC XY:

13735

AN XY:

83048

show subpopulations

Gnomad AFR exome

AF:

0.0660

Gnomad AMR exome

AF:

0.117

Gnomad ASJ exome

AF:

0.207

Gnomad EAS exome

AF:

0.0483

Gnomad SAS exome

AF:

0.0913

Gnomad FIN exome

AF:

0.279

Gnomad NFE exome

AF:

0.215

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.200

AC:

279555

AN:

1399088

Hom.:

29597

Cov.:

AF XY:

0.197

AC XY:

135724

AN XY:

690048

show subpopulations

Gnomad4 AFR exome

AF:

0.0662

Gnomad4 AMR exome

AF:

0.123

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.0739

Gnomad4 SAS exome

AF:

0.0889

Gnomad4 FIN exome

AF:

0.281

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.162

AC:

24611

AN:

151914

Hom.:

2384

Cov.:

AF XY:

0.161

AC XY:

11970

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.0748

Gnomad4 AMR

AF:

0.134

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.0581

Gnomad4 SAS

AF:

0.0885

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.217

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.202

Hom.:

2403

Bravo

AF:

0.148

TwinsUK

AF:

0.217

AC:

806

ALSPAC

AF:

0.215

AC:

829

ESP6500AA

AF:

0.0824

AC:

114

ESP6500EA

AF:

0.209

AC:

666

ExAC

AF:

0.153

AC:

3841

Asia WGS

AF:

0.0750

AC:

262

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 03, 2014	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2011	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Retinitis pigmentosa

Benign:2

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Retinitis pigmentosa 25

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Retinal dystrophy

Benign:1

Benign, criteria provided, single submitter

research

Dept Of Ophthalmology, Nagoya University

Oct 01, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.30

Cadd

Benign

Dann

Uncertain

0.99

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.33

LIST_S2

Benign

0.44

T;T

MetaRNN

Benign

0.0046

T;T

MetaSVM

Benign

-0.48

MutationAssessor

Pathogenic

3.4

M;M

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.26

PROVEAN

Pathogenic

-4.4

D;D

REVEL

Uncertain

0.40

Sift

Uncertain

0.0060

D;D

Sift4G

Pathogenic

0.0

D;D

Polyphen

0.97

D;.

Vest4

0.30

MPC

0.057

ClinPred

0.053

GERP RS

0.45

Varity_R

0.20

gMVP

0.77

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