rs34154043

Variant names:

• chr6-65405388-GA-G
• rs34154043
• NM_001142800.2:c.863-22delT

Your query was ambiguous. Multiple possible variants found:

• chr6-65405388-GA-G
• chr6-65405388-GA-GAA
• chr6-65405388-GA-GAAA
• chr6-65405388-GA-GAAAA
• chr6-65405388-GA-GAAAAA
• chr6-65405388-GA-GAAAAAA
• chr6-65405388-GA-GAAAAAAA
• chr6-65405388-GA-GAAAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001142800.2(EYS):​c.863-22delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00297 in 1,485,430 control chromosomes in the GnomAD database, including 27 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0023 (3 hom., cov: 0)
  • Exomes 𝑓: 0.0030 (24 hom.)
• Consequence: EYS NM_001142800.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYS	NM_001142800.2	c.863-22delT		intron_variant	Intron 5 of 42	ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2	c.863-22delT		intron_variant	Intron 5 of 43		NP_001278938.1
EYS	NM_001142801.2	c.863-22delT		intron_variant	Intron 5 of 11		NP_001136273.1
EYS	NM_198283.2	c.863-22delT		intron_variant	Intron 4 of 9		NP_938024.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.863-22delT		intron_variant	Intron 5 of 42	5	NM_001142800.2	ENSP00000424243.1
EYS	ENST00000370621.7	c.863-22delT		intron_variant	Intron 5 of 43	1		ENSP00000359655.3
EYS	ENST00000393380.6	c.863-22delT		intron_variant	Intron 5 of 11	1		ENSP00000377042.2
EYS	ENST00000342421.9	c.863-22delT		intron_variant	Intron 3 of 8	1		ENSP00000341818.5

Frequencies

GnomAD3 genomes AF: 0.00233 AC: 345 AN: 148276 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.000570

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00552

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000211

Gnomad FIN AF: 0.000420

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00337

Gnomad OTH AF: 0.00294

GnomAD3 exomes AF: 0.00246 AC: 499 AN: 202572 Hom.: 12 AF XY: 0.00256 AC XY: 283 AN XY: 110630

Gnomad AFR exome AF: 0.000808

Gnomad AMR exome AF: 0.00401

Gnomad ASJ exome AF: 0.00125

Gnomad EAS exome AF: 0.0000692

Gnomad SAS exome AF: 0.00117

Gnomad FIN exome AF: 0.000325

Gnomad NFE exome AF: 0.00340

Gnomad OTH exome AF: 0.00403

GnomAD4 exome AF: 0.00304 AC: 4064 AN: 1337052 Hom.: 24 Cov.: 25 AF XY: 0.00305 AC XY: 2039 AN XY: 669014

Gnomad4 AFR exome AF: 0.000499

Gnomad4 AMR exome AF: 0.00363

Gnomad4 ASJ exome AF: 0.00103

Gnomad4 EAS exome AF: 0.0000791

Gnomad4 SAS exome AF: 0.00109

Gnomad4 FIN exome AF: 0.000505

Gnomad4 NFE exome AF: 0.00352

Gnomad4 OTH exome AF: 0.00322

GnomAD4 genome AF: 0.00233 AC: 345 AN: 148378 Hom.: 3 Cov.: 0 AF XY: 0.00251 AC XY: 181 AN XY: 72244

Gnomad4 AFR AF: 0.000568

Gnomad4 AMR AF: 0.00551

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000212

Gnomad4 FIN AF: 0.000420

Gnomad4 NFE AF: 0.00337

Gnomad4 OTH AF: 0.00291

Alfa AF: 0.00204 Hom.: 270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34154043; hg19: chr6-66115281;