NM_004100.5:c.237A>G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong

The NM_004100.5(EYA4):c.237A>G(p.Ala79Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A79A) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

EYA4
NM_004100.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.75

Publications

1 publications found

Variant links:

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]

EYA4 Gene-Disease associations (from GenCC):

autosomal dominant nonsyndromic hearing loss 10
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia
nonsyndromic genetic hearing loss
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
autosomal dominant nonsyndromic hearing loss
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
dilated cardiomyopathy 1J
Inheritance: AD Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen

EYA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 6-133448139-A-G is Benign according to our data. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-133448139-A-G is described in CliVar as Likely_benign. Clinvar id is 179394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EYA4	NM_004100.5 link	c.237A>G	p.Ala79Ala	synonymous_variant	Exon 5 of 20	ENST00000355286.12	NP_004091.3	O95677-1Q96CJ7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EYA4	ENST00000355286.12 link	c.237A>G	p.Ala79Ala	synonymous_variant	Exon 5 of 20	1	NM_004100.5	ENSP00000347434.7		O95677-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251448

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1461582

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

727096

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33468

American (AMR)

AF:

0.0000447

AC:

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26128

East Asian (EAS)

AF:

0.00

AC:

AN:

39686

South Asian (SAS)

AF:

0.00

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53416

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111758

Other (OTH)

AF:

0.00

AC:

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Nov 26, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Ala79Ala in exon 5 of EYA4: This variant is not expected to have clinical signif icance because it does not alter an amino acid residue and is not located within the splice consensus sequence. -

Dilated cardiomyopathy 1J

Benign:1

Nov 28, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.36

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.36

Position offset: 40

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over