rs9375955

Positions:

• chr6-133303272-T-C
• chr6-133303272-T-G

Variant summary

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

The NM_004100.5(EYA4):​c.33+28459T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,282 control chromosomes in the GnomAD database, including 1,360 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 0.12 (1360 hom., cov: 32)
• Consequence: EYA4 NM_004100.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

EYA4 (HGNC:3522): (EYA transcriptional coactivator and phosphatase 4) This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may act as a transcriptional activator through its protein phosphatase activity, and it may be important for eye development, and for continued function of the mature organ of Corti. Mutations in this gene are associated with postlingual, progressive, autosomal dominant hearing loss at the deafness, autosomal dominant non-syndromic sensorineural 10 locus. The encoded protein is also a putative oncogene that mediates DNA repair, apoptosis, and innate immunity following DNA damage, cellular damage, and viral attack. Defects in this gene are also associated with dilated cardiomyopathy 1J. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

LOC124901403 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EYA4	NM_004100.5	c.33+28459T>C		intron_variant		ENST00000355286.12
LOC124901403	XR_007059773.1	n.2619T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EYA4	ENST00000355286.12	c.33+28459T>C		intron_variant		1	NM_004100.5	P4

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18125 AN: 152164 Hom.: 1361 Cov.: 32

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.119 AC: 18116 AN: 152282 Hom.: 1360 Cov.: 32 AF XY: 0.119 AC XY: 8827 AN XY: 74448

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0830 Hom.: 131

Bravo AF: 0.113

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.86

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

Other links and lift over

dbSNP: rs9375955; hg19: chr6-133624410;