chr6-64952728-A-G

Position:

• chr6-64952728-A-G

Variant summary

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

The NM_001142800.2(EYS):​c.2260-6814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,040 control chromosomes in the GnomAD database, including 3,230 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 (3230 hom., cov: 32)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EYS	NM_001142800.2	c.2260-6814T>C		intron_variant		ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2	c.2260-6814T>C		intron_variant			NP_001278938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.2260-6814T>C		intron_variant		5	NM_001142800.2	ENSP00000424243	A2
EYS	ENST00000370621.7	c.2260-6814T>C		intron_variant		1		ENSP00000359655	P2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30273 AN: 151924 Hom.: 3231 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.199 AC: 30283 AN: 152040 Hom.: 3230 Cov.: 32 AF XY: 0.200 AC XY: 14831 AN XY: 74332

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.191

Alfa AF: 0.212 Hom.: 4695

Bravo AF: 0.188

Asia WGS AF: 0.178 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.50

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: rs7767572; hg19: chr6-65662621; COSMIC: COSV65538142;