chr8-71351721-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_000503.6(EYA1):​c.124+3061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,210 control chromosomes in the GnomAD database, including 53,098 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 0.83 ( 53098 hom., cov: 33)

Consequence

EYA1
NM_000503.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EYA1NM_000503.6 linkc.124+3061G>A intron_variant ENST00000340726.8 NP_000494.2 Q99502-1A0A024R813B3KXR1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EYA1ENST00000340726.8 linkc.124+3061G>A intron_variant 1 NM_000503.6 ENSP00000342626.3 Q99502-1

Frequencies

GnomAD3 genomes
AF:
0.835
AC:
126993
AN:
152092
Hom.:
53072
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.829
Gnomad AMI
AF:
0.867
Gnomad AMR
AF:
0.876
Gnomad ASJ
AF:
0.860
Gnomad EAS
AF:
0.837
Gnomad SAS
AF:
0.796
Gnomad FIN
AF:
0.857
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.826
Gnomad OTH
AF:
0.850
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.835
AC:
127075
AN:
152210
Hom.:
53098
Cov.:
33
AF XY:
0.837
AC XY:
62274
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.828
Gnomad4 AMR
AF:
0.877
Gnomad4 ASJ
AF:
0.860
Gnomad4 EAS
AF:
0.837
Gnomad4 SAS
AF:
0.794
Gnomad4 FIN
AF:
0.857
Gnomad4 NFE
AF:
0.826
Gnomad4 OTH
AF:
0.851
Alfa
AF:
0.830
Hom.:
109930
Bravo
AF:
0.835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.29
CADD
Benign
18
DANN
Benign
0.65

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: rs2218488; hg19: chr8-72263956; API