rs13263568

Variant summary

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

The ENST00000523987.4(EYA1):​n.248+561A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 152,286 control chromosomes in the GnomAD database, including 498 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 0.072 ( 498 hom., cov: 32)

Consequence

EYA1
ENST00000523987.4 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.09
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]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EYA1NM_001370333.1 linkuse as main transcriptc.33+561A>C intron_variant
EYA1NM_001370334.1 linkuse as main transcriptc.-129+561A>C intron_variant
EYA1NM_001370335.1 linkuse as main transcriptc.-344+561A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EYA1ENST00000523987.4 linkuse as main transcriptn.248+561A>C intron_variant, non_coding_transcript_variant 1
EYA1ENST00000643681.1 linkuse as main transcriptc.33+561A>C intron_variant
EYA1ENST00000644229.1 linkuse as main transcriptc.33+561A>C intron_variant

Frequencies

GnomAD3 genomes
AF:
0.0720
AC:
10961
AN:
152168
Hom.:
499
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0312
Gnomad AMI
AF:
0.0811
Gnomad AMR
AF:
0.0613
Gnomad ASJ
AF:
0.0573
Gnomad EAS
AF:
0.121
Gnomad SAS
AF:
0.126
Gnomad FIN
AF:
0.0493
Gnomad MID
AF:
0.0506
Gnomad NFE
AF:
0.0960
Gnomad OTH
AF:
0.0712
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0719
AC:
10952
AN:
152286
Hom.:
498
Cov.:
32
AF XY:
0.0705
AC XY:
5250
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.0311
Gnomad4 AMR
AF:
0.0613
Gnomad4 ASJ
AF:
0.0573
Gnomad4 EAS
AF:
0.120
Gnomad4 SAS
AF:
0.125
Gnomad4 FIN
AF:
0.0493
Gnomad4 NFE
AF:
0.0960
Gnomad4 OTH
AF:
0.0724
Alfa
AF:
0.0903
Hom.:
370
Bravo
AF:
0.0685
Asia WGS
AF:
0.108
AC:
374
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.013
DANN
Benign
0.67

Splicing

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: rs13263568; hg19: chr8-72447418; API