6-64307084-TGAGAGAGAGAGA-TGAGAGAGAGA

Variant names:

Variant summary

Our verdict is Benign. The variant received -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

Publications

8 publications found

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 Gene-Disease associations (from GenCC):

EYS-related retinopathy
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
retinitis pigmentosa
Inheritance: AR, AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
retinitis pigmentosa 25
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

EYS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 196616.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142800.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EYS	NM_001142800.2	MANE Select	c.6079-4_6079-3delTC		splice_region intron	N/A	NP_001136272.1
	EYS	NM_001292009.2		c.6079-4_6079-3delTC		splice_region intron	N/A	NP_001278938.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EYS	ENST00000503581.6	TSL:5 MANE Select	c.6079-4_6079-3delTC		splice_region intron	N/A	ENSP00000424243.1
	EYS	ENST00000370621.7	TSL:1	c.6079-4_6079-3delTC		splice_region intron	N/A	ENSP00000359655.3

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

GnomAD2 exomes

AF:

0.551

AC:

51515

AN:

93566

AF XY:

0.546

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 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

African (AFR)

AF:

0.515

AC:

8945

AN:

17376

American (AMR)

AF:

0.506

AC:

13610

AN:

26882

Ashkenazi Jewish (ASJ)

AF:

0.528

AC:

10066

AN:

19080

East Asian (EAS)

AF:

0.474

AC:

13416

AN:

28278

South Asian (SAS)

AF:

0.519

AC:

29973

AN:

57746

European-Finnish (FIN)

AF:

0.532

AC:

22719

AN:

42686

Middle Eastern (MID)

AF:

0.580

AC:

2363

AN:

4074

European-Non Finnish (NFE)

AF:

0.515

AC:

247515

AN:

480314

Other (OTH)

AF:

0.517

AC:

17743

AN:

34314

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.611

Heterozygous variant carriers

8539

17079

25618

34158

42697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4802

9604

14406

19208

24010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.680

AC:

101929

AN:

149830

Hom.:

34426

Cov.:

AF XY:

0.676

AC XY:

49371

AN XY:

73020

show subpopulations

African (AFR)

AF:

0.673

AC:

27562

AN:

40958

American (AMR)

AF:

0.672

AC:

10091

AN:

15010

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2497

AN:

3458

East Asian (EAS)

AF:

0.488

AC:

2479

AN:

5084

South Asian (SAS)

AF:

0.707

AC:

3343

AN:

4730

European-Finnish (FIN)

AF:

0.643

AC:

6526

AN:

10150

Middle Eastern (MID)

AF:

0.637

AC:

186

AN:

292

European-Non Finnish (NFE)

AF:

0.706

AC:

47414

AN:

67176

Other (OTH)

AF:

0.670

AC:

1382

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1603

3205

4808

6410

8013

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.573

Hom.:

2265

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

Dec 03, 2021

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Jun 12, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not provided

Benign:2

Apr 11, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Retinitis Pigmentosa, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Retinitis pigmentosa

Benign:1

Sep 16, 2020

Natera, Inc.

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.76

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over