Variant 6-64307084-TGAGAGAGAGAGA-TGAGAGAGAGA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001142800.2(EYS):c.6079-4_6079-3delTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 860,580 control chromosomes in the GnomAD database, including 81,349 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 34426 hom., cov: 0)

Exomes 𝑓: 0.52 ( 46923 hom. )

Consequence

EYS
NM_001142800.2 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.762

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 -16 ACMG points.

BP6

Variant 6-64307084-TGA-T is Benign according to our data. Variant chr6-64307084-TGA-T is described in ClinVar as [Benign]. Clinvar id is 196616.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-64307084-TGA-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 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.6079-4_6079-3delTC		splice_region_variant, intron_variant		ENST00000503581.6	NP_001136272.1	Q5T1H1-1
EYS	NM_001292009.2 linkuse as main transcript	c.6079-4_6079-3delTC		splice_region_variant, intron_variant			NP_001278938.1	Q5T1H1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.6079-4_6079-3delTC		splice_region_variant, intron_variant		5	NM_001142800.2	ENSP00000424243.1		Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.6079-4_6079-3delTC		splice_region_variant, intron_variant		1		ENSP00000359655.3		Q5T1H1-3

Frequencies

GnomAD3 genomes

AF:

0.680

AC:

101866

AN:

149726

Hom.:

34406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.493

Gnomad AMR

AF:

0.673

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.487

Gnomad SAS

AF:

0.707

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.706

Gnomad OTH

AF:

0.668

GnomAD3 exomes

AF:

0.551

AC:

51515

AN:

93566

Hom.:

6275

AF XY:

0.546

AC XY:

27027

AN XY:

49492

show subpopulations

Gnomad AFR exome

AF:

0.565

Gnomad AMR exome

AF:

0.553

Gnomad ASJ exome

AF:

0.542

Gnomad EAS exome

AF:

0.503

Gnomad SAS exome

AF:

0.535

Gnomad FIN exome

AF:

0.573

Gnomad NFE exome

AF:

0.557

Gnomad OTH exome

AF:

0.548

GnomAD4 exome

AF:

0.515

AC:

366350

AN:

710750

Hom.:

46923

AF XY:

0.517

AC XY:

191570

AN XY:

370368

show subpopulations

Gnomad4 AFR exome

AF:

0.515

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.528

Gnomad4 EAS exome

AF:

0.474

Gnomad4 SAS exome

AF:

0.519

Gnomad4 FIN exome

AF:

0.532

Gnomad4 NFE exome

AF:

0.515

Gnomad4 OTH exome

AF:

0.517

GnomAD4 genome

AF:

0.680

AC:

101929

AN:

149830

Hom.:

34426

Cov.:

AF XY:

0.676

AC XY:

49371

AN XY:

73020

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.672

Gnomad4 ASJ

AF:

0.722

Gnomad4 EAS

AF:

0.488

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.643

Gnomad4 NFE

AF:

0.706

Gnomad4 OTH

AF:

0.670

Bravo

AF:

0.677

ClinVar

Significance: Benign

Submissions summary: Benign:6

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)	Jun 12, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 03, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 11, 2018	- -

Retinitis Pigmentosa, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Retinitis pigmentosa

Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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