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GeneBe

8-71335939-T-C

Variant summary

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

The NM_000503.6(EYA1):c.125-1765A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,024 control chromosomes in the GnomAD database, including 9,547 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 0.34 ( 9547 hom., cov: 32)

Consequence

EYA1
NM_000503.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470
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=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EYA1NM_000503.6 linkuse as main transcriptc.125-1765A>G intron_variant ENST00000340726.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EYA1ENST00000340726.8 linkuse as main transcriptc.125-1765A>G intron_variant 1 NM_000503.6 P4Q99502-1

Frequencies

GnomAD3 genomes
AF:
0.339
AC:
51565
AN:
151906
Hom.:
9536
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.263
Gnomad AMI
AF:
0.463
Gnomad AMR
AF:
0.489
Gnomad ASJ
AF:
0.287
Gnomad EAS
AF:
0.723
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.281
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.328
Gnomad OTH
AF:
0.328
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.339
AC:
51612
AN:
152024
Hom.:
9547
Cov.:
32
AF XY:
0.345
AC XY:
25627
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.263
Gnomad4 AMR
AF:
0.490
Gnomad4 ASJ
AF:
0.287
Gnomad4 EAS
AF:
0.723
Gnomad4 SAS
AF:
0.427
Gnomad4 FIN
AF:
0.281
Gnomad4 NFE
AF:
0.328
Gnomad4 OTH
AF:
0.331
Alfa
AF:
0.331
Hom.:
12213
Bravo
AF:
0.353
Asia WGS
AF:
0.563
AC:
1957
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
5.7
Dann
Benign
0.82

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: rs3779748; hg19: chr8-72248174; API