rs1156154

Variant names:

• chr8-71571748-G-A
• rs1156154
• ENST00000518177.2:n.76-2821C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-71571748-G-A
• chr8-71571748-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000518177.2(EYA1):​n.76-2821C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 6 publications found

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]

EYA1 Gene-Disease associations (from GenCC):

• branchio-oto-renal syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• branchiootorenal syndrome 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• branchiootic syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia
• branchiootic syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000303523 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYA1	ENST00000518177.2	n.76-2821C>T		intron_variant	Intron 1 of 3	2
EYA1	ENST00000521794.1	n.83-2821C>T		intron_variant	Intron 1 of 1	2
ENSG00000303523	ENST00000795262.1	n.167+18104G>A		intron_variant	Intron 2 of 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

African (AFR) AF: 0.783 AC: 32426 AN: 41406

American (AMR) AF: 0.580 AC: 8837 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1432 AN: 3466

East Asian (EAS) AF: 0.757 AC: 3897 AN: 5148

South Asian (SAS) AF: 0.585 AC: 2813 AN: 4810

European-Finnish (FIN) AF: 0.478 AC: 5029 AN: 10520

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30099 AN: 67864

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.489 Hom.: 59946

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1156154; hg19: chr8-72483983;