GeneBe

6-65405388-GA-GAAAAAAAAAAAAAAAAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001142800.2(EYS):​c.863-22_863-21insTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000748 in 1,337,228 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 7.5e-7 ( 0 hom. )

Consequence

EYS
NM_001142800.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.391

Publications

0 publications found
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]
EYS Gene-Disease associations (from GenCC):
  • EYS-related retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa
    Inheritance: AR, AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
  • retinitis pigmentosa 25
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EYSNM_001142800.2 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 42 ENST00000503581.6 NP_001136272.1 Q5T1H1-1
EYSNM_001292009.2 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 43 NP_001278938.1 Q5T1H1-3
EYSNM_001142801.2 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 11 NP_001136273.1 Q5T1H1-4
EYSNM_198283.2 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 4 of 9 NP_938024.1 Q5T1H1-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EYSENST00000503581.6 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 42 5 NM_001142800.2 ENSP00000424243.1 Q5T1H1-1
EYSENST00000370621.7 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 43 1 ENSP00000359655.3 Q5T1H1-3
EYSENST00000393380.6 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 5 of 11 1 ENSP00000377042.2 Q5T1H1-4
EYSENST00000342421.9 linkc.863-22_863-21insTTTTTTTTTTTTTTTTT intron_variant Intron 3 of 8 1 ENSP00000341818.5 Q5T1H1-2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
7.48e-7
AC:
1
AN:
1337228
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
669120
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
30074
American (AMR)
AF:
0.00
AC:
0
AN:
38308
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24174
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37926
South Asian (SAS)
AF:
0.00
AC:
0
AN:
77012
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51442
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5340
European-Non Finnish (NFE)
AF:
9.83e-7
AC:
1
AN:
1017378
Other (OTH)
AF:
0.00
AC:
0
AN:
55574
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.39

Splicing

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

Publications

Other links and lift over

dbSNP: rs34154043; hg19: chr6-66115281; API