rs10094908

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000340726.8(EYA1):​c.556+2180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,124 control chromosomes in the GnomAD database, including 3,020 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 0.19 ( 3020 hom., cov: 33)

Consequence

EYA1
ENST00000340726.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0870
Variant links:
Genes affected
EYA1 (HGNC:3519): (EYA transcriptional coactivator and phosphatase 1) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may play a role in the developing kidney, branchial arches, eye, and ear. Mutations of this gene have been associated with branchiootorenal dysplasia syndrome, branchiootic syndrome, and sporadic cases of congenital cataracts and ocular anterior segment anomalies. A similar protein in mice can act as a transcriptional activator. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Dec 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EYA1NM_000503.6 linkuse as main transcriptc.556+2180C>T intron_variant ENST00000340726.8 NP_000494.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EYA1ENST00000340726.8 linkuse as main transcriptc.556+2180C>T intron_variant 1 NM_000503.6 ENSP00000342626 P4Q99502-1

Frequencies

GnomAD3 genomes
AF:
0.185
AC:
28192
AN:
152006
Hom.:
3023
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.111
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.170
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.248
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.239
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.185
AC:
28184
AN:
152124
Hom.:
3020
Cov.:
33
AF XY:
0.184
AC XY:
13705
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.150
Gnomad4 ASJ
AF:
0.154
Gnomad4 EAS
AF:
0.170
Gnomad4 SAS
AF:
0.183
Gnomad4 FIN
AF:
0.248
Gnomad4 NFE
AF:
0.239
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.216
Hom.:
417
Bravo
AF:
0.172
Asia WGS
AF:
0.188
AC:
652
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.6
DANN
Benign
0.69

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10094908; hg19: chr8-72227607; API