rs371802597

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004086.3(COCH):​c.73G>A​(p.Glu25Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000422 in 1,422,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000042 ( 0 hom. )

Consequence

COCH
NM_004086.3 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.871
Variant links:
Genes affected
COCH (HGNC:2180): (cochlin) The protein encoded by this gene is highly conserved in human, mouse, and chicken, showing 94% and 79% amino acid identity of human to mouse and chicken sequences, respectively. Hybridization to this gene was detected in spindle-shaped cells located along nerve fibers between the auditory ganglion and sensory epithelium. These cells accompany neurites at the habenula perforata, the opening through which neurites extend to innervate hair cells. This and the pattern of expression of this gene in chicken inner ear paralleled the histologic findings of acidophilic deposits, consistent with mucopolysaccharide ground substance, in temporal bones from DFNA9 (autosomal dominant nonsyndromic sensorineural deafness 9) patients. Mutations that cause DFNA9 have been reported in this gene. Alternative splicing results in multiple transcript variants encoding the same protein. Additional splice variants encoding distinct isoforms have been described but their biological validities have not been demonstrated. [provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15473795).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COCHNM_004086.3 linkc.73G>A p.Glu25Lys missense_variant Exon 3 of 12 ENST00000396618.9 NP_004077.1 O43405-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COCHENST00000396618.9 linkc.73G>A p.Glu25Lys missense_variant Exon 3 of 12 1 NM_004086.3 ENSP00000379862.3 O43405-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000422
AC:
6
AN:
1422348
Hom.:
0
Cov.:
32
AF XY:
0.00000426
AC XY:
3
AN XY:
704248
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000549
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000122
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.093
BayesDel_addAF
Benign
-0.033
T
BayesDel_noAF
Benign
-0.29
CADD
Benign
19
DANN
Uncertain
1.0
DEOGEN2
Benign
0.039
.;T;T;.;.;T;T
Eigen
Benign
-0.19
Eigen_PC
Benign
-0.040
FATHMM_MKL
Uncertain
0.80
D
LIST_S2
Benign
0.43
T;.;.;T;T;T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.15
T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
.;N;N;.;N;.;N
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
-0.020
N;N;.;.;N;N;.
REVEL
Benign
0.11
Sift
Uncertain
0.023
D;D;.;.;D;D;.
Sift4G
Benign
0.74
T;T;.;.;T;T;.
Polyphen
0.48
.;P;P;.;.;.;P
Vest4
0.20
MVP
0.73
MPC
0.25
ClinPred
0.32
T
GERP RS
4.5
Varity_R
0.24
gMVP
0.33

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: rs371802597; hg19: chr14-31344300; COSMIC: COSV105084042; COSMIC: COSV105084042; API