Variant rs36133910 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.6078+68A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,345,756 control chromosomes in the GnomAD database, including 60,109 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 5960 hom., cov: 32)

Exomes 𝑓: 0.30 ( 54149 hom. )

Consequence

EYS
NM_001142800.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.562

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:

(HGNC:):

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=-0.86).

BP6

Variant 6-64388622-T-C is Benign according to our data. Variant chr6-64388622-T-C is described in ClinVar as [Benign]. Clinvar id is 1175357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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.6078+68A>G		intron_variant		ENST00000503581.6
EYS	NM_001292009.2 linkuse as main transcript	c.6078+68A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.6078+68A>G	intron_variant	5	NM_001142800.2	A2	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.6078+68A>G	intron_variant	1		P2	Q5T1H1-3
	ENST00000424274.1 linkuse as main transcript	n.267+8910T>C	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42119

AN:

151888

Hom.:

5956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.464

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.349

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.298

AC:

356260

AN:

1193748

Hom.:

54149

AF XY:

0.298

AC XY:

175928

AN XY:

589550

show subpopulations

Gnomad4 AFR exome

AF:

0.205

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.289

Gnomad4 EAS exome

AF:

0.459

Gnomad4 SAS exome

AF:

0.291

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.294

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.277

AC:

42147

AN:

152008

Hom.:

5960

Cov.:

AF XY:

0.281

AC XY:

20862

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.284

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.464

Gnomad4 SAS

AF:

0.289

Gnomad4 FIN

AF:

0.349

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.273

Hom.:

698

Bravo

AF:

0.275

Asia WGS

AF:

0.348

AC:

1205

AN:

3456

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

-0.86

CADD

Benign

0.36

DANN

Benign

0.71

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