rs9342097

chr6-64011163-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142800.2(EYS):c.6726-11980A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,012 control chromosomes in the GnomAD database, including 7,729 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 0.31 (7729 hom., cov: 32)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

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]

LOC107986608 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EYS	NM_001142800.2	c.6726-11980A>C		intron_variant		ENST00000503581.6
LOC107986608	XR_007059629.1	n.317-10224T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EYS	ENST00000503581.6	c.6726-11980A>C		intron_variant		5	NM_001142800.2	A2
EYS	ENST00000370621.7	c.6726-11980A>C		intron_variant		1		P2
EYS	ENST00000398580.3	c.40-11980A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47734 AN: 151894 Hom.: 7724 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.351

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.314 AC: 47752 AN: 152012 Hom.: 7729 Cov.: 32 AF XY: 0.311 AC XY: 23085 AN XY: 74300

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.346

Alfa AF: 0.350 Hom.: 18615

Bravo AF: 0.310

Asia WGS AF: 0.326 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	8.8
Dann	Benign	0.76

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

Other links and lift over

dbSNP: rs9342097; hg19: chr6-64721056;