Variant 6-65295847-GAA-GAAA 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.2023+15dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 22197 hom., cov: 0)

Exomes 𝑓: 0.49 ( 87833 hom. )

Failed GnomAD Quality Control

Consequence

EYS
NM_001142800.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.679

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:

EYS (HGNC:):

EYS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 6-65295847-G-GA is Benign according to our data. Variant chr6-65295847-G-GA is described in ClinVar as [Benign]. Clinvar id is 357735.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 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.2023+15dupT		intron_variant		ENST00000503581.6	NP_001136272.1	Q5T1H1-1
EYS	NM_001292009.2 linkuse as main transcript	c.2023+15dupT		intron_variant			NP_001278938.1	Q5T1H1-3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
EYS	ENST00000503581.6 linkuse as main transcript	c.2023+15dupT	intron_variant		5	NM_001142800.2	ENSP00000424243.1	Q5T1H1-1
EYS	ENST00000370621.7 linkuse as main transcript	c.2023+15dupT	intron_variant		1		ENSP00000359655.3	Q5T1H1-3
EYS	ENST00000370615.3 linkuse as main transcript	n.476dupT	non_coding_transcript_exon_variant	2/2	3
EYS	ENST00000447127.1 linkuse as main transcript	n.494dupT	non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

77750

AN:

149522

Hom.:

22191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.735

Gnomad AMR

AF:

0.665

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.898

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.583

Gnomad OTH

AF:

0.579

GnomAD3 exomes

AF:

0.491

AC:

44607

AN:

90928

Hom.:

5973

AF XY:

0.486

AC XY:

23162

AN XY:

47616

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.567

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.655

Gnomad SAS exome

AF:

0.475

Gnomad FIN exome

AF:

0.498

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.482

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.491

AC:

600699

AN:

1223206

Hom.:

87833

Cov.:

AF XY:

0.492

AC XY:

296491

AN XY:

603158

show subpopulations

Gnomad4 AFR exome

AF:

0.277

Gnomad4 AMR exome

AF:

0.543

Gnomad4 ASJ exome

AF:

0.440

Gnomad4 EAS exome

AF:

0.643

Gnomad4 SAS exome

AF:

0.515

Gnomad4 FIN exome

AF:

0.482

Gnomad4 NFE exome

AF:

0.491

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.520

AC:

77766

AN:

149608

Hom.:

22197

Cov.:

AF XY:

0.527

AC XY:

38434

AN XY:

72962

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.665

Gnomad4 ASJ

AF:

0.513

Gnomad4 EAS

AF:

0.897

Gnomad4 SAS

AF:

0.677

Gnomad4 FIN

AF:

0.568

Gnomad4 NFE

AF:

0.583

Gnomad4 OTH

AF:

0.583

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 11, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	- -

Retinitis Pigmentosa, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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