rs13197839

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142800.2(EYS):​c.2023+16464T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,990 control chromosomes in the GnomAD database, including 3,512 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3512 hom., cov: 31)

Consequence

EYS
NM_001142800.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EYSNM_001142800.2 linkuse as main transcriptc.2023+16464T>G intron_variant ENST00000503581.6
EYSNM_001292009.2 linkuse as main transcriptc.2023+16464T>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EYSENST00000503581.6 linkuse as main transcriptc.2023+16464T>G intron_variant 5 NM_001142800.2 A2Q5T1H1-1
EYSENST00000370621.7 linkuse as main transcriptc.2023+16464T>G intron_variant 1 P2Q5T1H1-3

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29800
AN:
151872
Hom.:
3515
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0863
Gnomad AMI
AF:
0.114
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.344
Gnomad EAS
AF:
0.0583
Gnomad SAS
AF:
0.127
Gnomad FIN
AF:
0.327
Gnomad MID
AF:
0.266
Gnomad NFE
AF:
0.258
Gnomad OTH
AF:
0.178
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.196
AC:
29797
AN:
151990
Hom.:
3512
Cov.:
31
AF XY:
0.195
AC XY:
14522
AN XY:
74292
show subpopulations
Gnomad4 AFR
AF:
0.0861
Gnomad4 AMR
AF:
0.171
Gnomad4 ASJ
AF:
0.344
Gnomad4 EAS
AF:
0.0580
Gnomad4 SAS
AF:
0.128
Gnomad4 FIN
AF:
0.327
Gnomad4 NFE
AF:
0.258
Gnomad4 OTH
AF:
0.176
Alfa
AF:
0.240
Hom.:
2529
Bravo
AF:
0.179
Asia WGS
AF:
0.0970
AC:
339
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.1
DANN
Benign
0.62

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.

Other links and lift over

dbSNP: rs13197839; hg19: chr6-65989292; API