Variant rs7743515 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_001142800.2(EYS):c.2847-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 1,424,302 control chromosomes in the GnomAD database, including 470,811 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.83 ( 52440 hom., cov: 31)

Exomes 𝑓: 0.81 ( 418371 hom. )

Consequence

EYS
NM_001142800.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.904

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 (BayesDel_noAF=-0.9).

BP6

Variant 6-64886866-G-A is Benign according to our data. Variant chr6-64886866-G-A is described in ClinVar as [Benign]. Clinvar id is 1175362.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EYS	NM_001142800.2 linkuse as main transcript	c.2847-24C>T		intron_variant		ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2 linkuse as main transcript	c.2847-24C>T		intron_variant			NP_001278938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.2847-24C>T		intron_variant		5	NM_001142800.2	ENSP00000424243	A2	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.2847-24C>T		intron_variant		1		ENSP00000359655	P2	Q5T1H1-3

Frequencies

GnomAD3 genomes

AF:

0.831

AC:

126094

AN:

151762

Hom.:

52399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.844

Gnomad AMI

AF:

0.821

Gnomad AMR

AF:

0.849

Gnomad ASJ

AF:

0.797

Gnomad EAS

AF:

0.851

Gnomad SAS

AF:

0.833

Gnomad FIN

AF:

0.862

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.814

Gnomad OTH

AF:

0.835

GnomAD3 exomes

AF:

0.828

AC:

97661

AN:

117980

Hom.:

40481

AF XY:

0.824

AC XY:

51931

AN XY:

63016

show subpopulations

Gnomad AFR exome

AF:

0.849

Gnomad AMR exome

AF:

0.867

Gnomad ASJ exome

AF:

0.783

Gnomad EAS exome

AF:

0.848

Gnomad SAS exome

AF:

0.827

Gnomad FIN exome

AF:

0.859

Gnomad NFE exome

AF:

0.808

Gnomad OTH exome

AF:

0.812

GnomAD4 exome

AF:

0.810

AC:

1031007

AN:

1272422

Hom.:

418371

Cov.:

AF XY:

0.811

AC XY:

510918

AN XY:

630090

show subpopulations

Gnomad4 AFR exome

AF:

0.839

Gnomad4 AMR exome

AF:

0.863

Gnomad4 ASJ exome

AF:

0.782

Gnomad4 EAS exome

AF:

0.849

Gnomad4 SAS exome

AF:

0.829

Gnomad4 FIN exome

AF:

0.855

Gnomad4 NFE exome

AF:

0.804

Gnomad4 OTH exome

AF:

0.809

GnomAD4 genome

AF:

0.831

AC:

126193

AN:

151880

Hom.:

52440

Cov.:

AF XY:

0.833

AC XY:

61831

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.849

Gnomad4 ASJ

AF:

0.797

Gnomad4 EAS

AF:

0.851

Gnomad4 SAS

AF:

0.831

Gnomad4 FIN

AF:

0.862

Gnomad4 NFE

AF:

0.814

Gnomad4 OTH

AF:

0.835

Alfa

AF:

0.810

Hom.:

59004

Bravo

AF:

0.828

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Retinitis pigmentosa 25

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.25

DANN

Benign

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over