6-64307084-TGAGAGAGAGAGA-TGAGAGAGAGAGAGAGA

Position:

• chr6-64307084-TGAGAGAGAGAGA-TGAGAGAGAGAGAGAGA

Variant summary

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

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

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000082 (0 hom.)
• Consequence: EYS NM_001142800.2 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Likely benign criteria provided, single submitter 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-TGAGA is Benign according to our data. Variant chr6-64307084-T-TGAGA is described in ClinVar as [Likely_benign]. Clinvar id is 1086951.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.6079-3_6079-2insTCTC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000503581.6	NP_001136272.1
EYS	NM_001292009.2	c.6079-3_6079-2insTCTC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NP_001278938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EYS	ENST00000503581.6	c.6079-3_6079-2insTCTC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_001142800.2	ENSP00000424243	A2
EYS	ENST00000370621.7	c.6079-3_6079-2insTCTC		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000359655	P2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0000107 AC: 1 AN: 93566 Hom.: 0 AF XY: 0.0000202 AC XY: 1 AN XY: 49492

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000270

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000821 AC: 6 AN: 731202 Hom.: 0 Cov.: 0 AF XY: 0.0000105 AC XY: 4 AN XY: 381320

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000225

Gnomad4 NFE exome AF: 0.00000815

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 18, 2022

- -

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;