rs13260349

Variant summary

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

The ENST00000340726.8(EYA1):​c.1141-7603G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,104 control chromosomes in the GnomAD database, including 14,631 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 0.42 ( 14631 hom., cov: 33)

Consequence

EYA1
ENST00000340726.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.297
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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EYA1NM_000503.6 linkuse as main transcriptc.1141-7603G>A 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.1141-7603G>A intron_variant 1 NM_000503.6 ENSP00000342626 P4Q99502-1

Frequencies

GnomAD3 genomes
AF:
0.425
AC:
64533
AN:
151986
Hom.:
14617
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.570
Gnomad AMI
AF:
0.373
Gnomad AMR
AF:
0.344
Gnomad ASJ
AF:
0.424
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.211
Gnomad FIN
AF:
0.401
Gnomad MID
AF:
0.449
Gnomad NFE
AF:
0.397
Gnomad OTH
AF:
0.427
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.425
AC:
64578
AN:
152104
Hom.:
14631
Cov.:
33
AF XY:
0.419
AC XY:
31179
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.570
Gnomad4 AMR
AF:
0.343
Gnomad4 ASJ
AF:
0.424
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.211
Gnomad4 FIN
AF:
0.401
Gnomad4 NFE
AF:
0.397
Gnomad4 OTH
AF:
0.422
Alfa
AF:
0.413
Hom.:
4428
Bravo
AF:
0.425
Asia WGS
AF:
0.191
AC:
665
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.78
DANN
Benign
0.56

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: rs13260349; hg19: chr8-72136861; API