chr6-64307084-T-TGA

Position:

• chr6-64307084-T-TGA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001142800.2(EYS):​c.6079-4_6079-3dupTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00077 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00037 (0 hom.)
• Consequence: EYS NM_001142800.2 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter U:1 B:1
• Conservation: PhyloP100: -0.0860

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 -2 ACMG points.

• BP6: Variant 6-64307084-T-TGA is Benign according to our data. Variant chr6-64307084-T-TGA is described in ClinVar as [Benign]. Clinvar id is 790350.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EYS	NM_001142800.2	c.6079-4_6079-3dupTC		splice_region_variant, intron_variant		ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2	c.6079-4_6079-3dupTC		splice_region_variant, intron_variant			NP_001278938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.6079-4_6079-3dupTC		splice_region_variant, intron_variant		5	NM_001142800.2	ENSP00000424243.1
EYS	ENST00000370621.7	c.6079-4_6079-3dupTC		splice_region_variant, intron_variant		1		ENSP00000359655.3

Frequencies

GnomAD3 genomes AF: 0.000767 AC: 115 AN: 149968 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00191

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000266

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00216

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000327

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000748 AC: 70 AN: 93566 Hom.: 0 AF XY: 0.000707 AC XY: 35 AN XY: 49492

Gnomad AFR exome AF: 0.00286

Gnomad AMR exome AF: 0.00107

Gnomad ASJ exome AF: 0.000392

Gnomad EAS exome AF: 0.00237

Gnomad SAS exome AF: 0.000243

Gnomad FIN exome AF: 0.000701

Gnomad NFE exome AF: 0.000243

Gnomad OTH exome AF: 0.000725

GnomAD4 exome AF: 0.000372 AC: 272 AN: 730928 Hom.: 0 Cov.: 0 AF XY: 0.000320 AC XY: 122 AN XY: 381172

Gnomad4 AFR exome AF: 0.00185

Gnomad4 AMR exome AF: 0.000870

Gnomad4 ASJ exome AF: 0.000102

Gnomad4 EAS exome AF: 0.000860

Gnomad4 SAS exome AF: 0.000118

Gnomad4 FIN exome AF: 0.000270

Gnomad4 NFE exome AF: 0.000301

Gnomad4 OTH exome AF: 0.000536

GnomAD4 genome AF: 0.000766 AC: 115 AN: 150072 Hom.: 0 Cov.: 0 AF XY: 0.000738 AC XY: 54 AN XY: 73152

Gnomad4 AFR AF: 0.00190

Gnomad4 AMR AF: 0.000266

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00216

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000327

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Uncertain:1 Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Retinitis pigmentosa Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Natera, Inc.

Apr 16, 2020

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 03, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs35395170; hg19: chr6-65016977;