rs1482455

Variant names:

• chr6-63987928-G-A
• rs1482455
• NM_001142800.2:c.6835-3325C>T

Variant summary

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

The NM_001142800.2(EYS):​c.6835-3325C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,250 control chromosomes in the GnomAD database, including 11,145 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 0.38 (11145 hom., cov: 31)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYS	NM_001142800.2	c.6835-3325C>T		intron_variant	Intron 34 of 42	ENST00000503581.6	NP_001136272.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.6835-3325C>T		intron_variant	Intron 34 of 42	5	NM_001142800.2	ENSP00000424243.1
EYS	ENST00000370621.7	c.6835-3325C>T		intron_variant	Intron 34 of 43	1		ENSP00000359655.3
EYS	ENST00000398580.3	c.148-3325C>T		intron_variant	Intron 2 of 9	5		ENSP00000381585.3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57255 AN: 151132 Hom.: 11136 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.379 AC: 57312 AN: 151250 Hom.: 11145 Cov.: 31 AF XY: 0.372 AC XY: 27502 AN XY: 73882

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.390

Alfa AF: 0.363 Hom.: 20314

Bravo AF: 0.383

Asia WGS AF: 0.363 AC: 1262 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	0.86
DANN	Benign	0.58

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: rs1482455; hg19: chr6-64697821;