rs1156154

chr8-71571748-G-Achr8-71571748-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518177.2(EYA1):n.76-2821C>T 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 0.568 in 151,758 control chromosomes in the GnomAD database, including 26,138 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 0.57 (26138 hom., cov: 31)
• Consequence: EYA1 ENST00000518177.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EYA1	ENST00000518177.2	n.76-2821C>T		intron_variant, non_coding_transcript_variant		2
EYA1	ENST00000521794.1	n.83-2821C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86153 AN: 151640 Hom.: 26091 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.568 AC: 86261 AN: 151758 Hom.: 26138 Cov.: 31 AF XY: 0.571 AC XY: 42358 AN XY: 74174

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.556

Alfa AF: 0.467 Hom.: 34546

Bravo AF: 0.586

Asia WGS AF: 0.633 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.50
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1156154; hg19: chr8-72483983;