Genetic Variant NM_001142800.2:c.977G>A (chr6-65405253-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001142800.2(EYS):c.977G>A(p.Ser326Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,613,202 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0036 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0013 ( 7 hom. )

Consequence

EYS
NM_001142800.2 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:6B:8

Conservation

PhyloP100: 0.120

Publications

7 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: Labcorp Genetics (formerly Invitae), Ambry Genetics, 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006911695).

BP6

Variant 6-65405253-C-T is Benign according to our data. Variant chr6-65405253-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 438211.

BS1

Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.00132 (1926/1461240) while in subpopulation MID AF = 0.0111 (64/5762). AF 95% confidence interval is 0.00893. There are 7 homozygotes in GnomAdExome4. There are 952 alleles in the male GnomAdExome4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 2 AR,AD gene

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
EYS	NM_001142800.2	MANE Select	c.977G>A	p.Ser326Asn	missense	Exon 6 of 43	NP_001136272.1	Q5T1H1-1
EYS	NM_001292009.2		c.977G>A	p.Ser326Asn	missense	Exon 6 of 44	NP_001278938.1	Q5T1H1-3
EYS	NM_001142801.2		c.977G>A	p.Ser326Asn	missense	Exon 6 of 12	NP_001136273.1	Q5T1H1-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
EYS	ENST00000503581.6	TSL:5 MANE Select	c.977G>A	p.Ser326Asn	missense	Exon 6 of 43	ENSP00000424243.1	Q5T1H1-1
EYS	ENST00000370621.7	TSL:1	c.977G>A	p.Ser326Asn	missense	Exon 6 of 44	ENSP00000359655.3	Q5T1H1-3
EYS	ENST00000393380.6	TSL:1	c.977G>A	p.Ser326Asn	missense	Exon 6 of 12	ENSP00000377042.2	Q5T1H1-4

Frequencies

GnomAD3 genomes

AF:

0.00356

AC:

541

AN:

151844

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00812

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00454

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00156

Gnomad OTH

AF:

0.00526

GnomAD2 exomes

AF:

0.00177

AC:

445

AN:

250760

AF XY:

0.00165

show subpopulations

Gnomad AFR exome

AF:

0.00818

Gnomad AMR exome

AF:

0.00295

Gnomad ASJ exome

AF:

0.00119

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00140

Gnomad OTH exome

AF:

0.00556

GnomAD4 exome

AF:

0.00132

AC:

1926

AN:

1461240

Hom.:

Cov.:

AF XY:

0.00131

AC XY:

952

AN XY:

726932

show subpopulations

African (AFR)

AF:

0.00757

AC:

253

AN:

33442

American (AMR)

AF:

0.00378

AC:

169

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.000919

AC:

AN:

26110

East Asian (EAS)

AF:

0.00

AC:

AN:

39620

South Asian (SAS)

AF:

0.000174

AC:

AN:

86242

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.0111

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00111

AC:

1238

AN:

1111600

Other (OTH)

AF:

0.00270

AC:

163

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

105

210

314

419

524

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.00355

AC:

540

AN:

151962

Hom.:

Cov.:

AF XY:

0.00349

AC XY:

259

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.00810

AC:

336

AN:

41500

American (AMR)

AF:

0.00453

AC:

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5162

South Asian (SAS)

AF:

0.000208

AC:

AN:

4810

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10586

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00156

AC:

106

AN:

67886

Other (OTH)

AF:

0.00521

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

114

143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00198

Hom.:

Bravo

AF:

0.00406

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.00613

AC:

ESP6500EA

AF:

0.00128

AC:

ExAC

AF:

0.00185

AC:

224

Asia WGS

AF:

0.000868

AC:

AN:

3472

EpiCase

AF:

0.00186

EpiControl

AF:

0.00196

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Retinitis pigmentosa (3)

Retinitis pigmentosa 25 (3)

not specified (2)

Retinal dystrophy (2)

Autosomal recessive retinitis pigmentosa (1)

EYS-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.52

CADD

Benign

0.30

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.032

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.017

LIST_S2

Benign

0.39

M_CAP

Uncertain

0.12

MetaRNN

Benign

0.0069

MetaSVM

Benign

-0.83

MutationAssessor

Benign

0.045

PhyloP100

0.12

PrimateAI

Benign

0.23

PROVEAN

Benign

0.030

REVEL

Benign

0.12

Sift

Uncertain

0.020

Sift4G

Benign

0.12

Polyphen

0.0010

Vest4

0.16

MVP

0.27

MPC

0.0098

ClinPred

0.0011

GERP RS

-1.7

Varity_R

0.054

gMVP

0.13

Mutation Taster

=4/96

disease causing

(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

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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

Computational scores

Splicing

Publications

Other links and lift over