rs6094514
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005244.5(EYA2):c.-11+40094C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,176 control chromosomes in the GnomAD database, including 1,552 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.13 ( 1552 hom., cov: 32)
Consequence
EYA2
NM_005244.5 intron
NM_005244.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.288
Genes affected
EYA2 (HGNC:3520): (EYA transcriptional coactivator and phosphatase 2) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may be post-translationally modified and may play a role in eye development. A similar protein in mice can act as a transcriptional activator. Alternative splicing results in multiple transcript variants, but the full-length natures of all of these variants have not yet been determined. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EYA2 | NM_005244.5 | c.-11+40094C>T | intron_variant | ENST00000327619.10 | |||
EYA2 | NM_172110.4 | c.-11+40094C>T | intron_variant | ||||
EYA2 | XM_005260327.3 | c.-11+40094C>T | intron_variant | ||||
EYA2 | XM_017027721.3 | c.-11+40094C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EYA2 | ENST00000327619.10 | c.-11+40094C>T | intron_variant | 2 | NM_005244.5 | P1 | |||
EYA2 | ENST00000357410.7 | c.-11+40094C>T | intron_variant | 1 | |||||
EYA2 | ENST00000497062.6 | c.-11+40094C>T | intron_variant | 1 | |||||
EYA2 | ENST00000611592.4 | c.-11+40094C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.129 AC: 19691AN: 152058Hom.: 1550 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.130 AC: 19708AN: 152176Hom.: 1552 Cov.: 32 AF XY: 0.129 AC XY: 9624AN XY: 74394
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at