GeneBe

rs35395170

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_001142800.2(EYS):​c.6079-14_6079-3del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 731,206 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

EYS
NM_001142800.2 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.937
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-64307084-TGAGAGAGAGAGA-T is Benign according to our data. Variant chr6-64307084-TGAGAGAGAGAGA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1566215.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EYSNM_001142800.2 linkuse as main transcriptc.6079-14_6079-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000503581.6 NP_001136272.1
EYSNM_001292009.2 linkuse as main transcriptc.6079-14_6079-3del 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
EYSENST00000503581.6 linkuse as main transcriptc.6079-14_6079-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 5 NM_001142800.2 ENSP00000424243 A2Q5T1H1-1
EYSENST00000370621.7 linkuse as main transcriptc.6079-14_6079-3del splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 ENSP00000359655 P2Q5T1H1-3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000274
AC:
2
AN:
731206
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
381320
show subpopulations
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:
0.00
Gnomad4 NFE exome
AF:
0.00000407
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 20, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-65016977; API