rs3857532

Positions:

• chr6-64523772-G-A
• chr6-64523772-G-C

Variant summary

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

The NM_001142800.2(EYS):​c.5644+66451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,428 control chromosomes in the GnomAD database, including 13,592 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 0.42 (13592 hom., cov: 32)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EYS	NM_001142800.2	c.5644+66451C>T		intron_variant		ENST00000503581.6
EYS	NM_001292009.2	c.5644+66451C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EYS	ENST00000503581.6	c.5644+66451C>T		intron_variant		5	NM_001142800.2	A2
EYS	ENST00000370621.7	c.5644+66451C>T		intron_variant		1		P2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62776 AN: 151308 Hom.: 13567 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.415 AC: 62857 AN: 151428 Hom.: 13592 Cov.: 32 AF XY: 0.415 AC XY: 30687 AN XY: 73982

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.399

Alfa AF: 0.372 Hom.: 1845

Bravo AF: 0.424

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.25

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: rs3857532; hg19: chr6-65233665;