14-30877360-G-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004086.3(COCH):​c.83-212G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 586,844 control chromosomes in the GnomAD database, including 124,435 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 29707 hom., cov: 31)
Exomes 𝑓: 0.66 ( 94728 hom. )

Consequence

COCH
NM_004086.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.499
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 Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant 14-30877360-G-C is Benign according to our data. Variant chr14-30877360-G-C is described in ClinVar as [Benign]. Clinvar id is 1251904.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COCHNM_004086.3 linkuse as main transcriptc.83-212G>C intron_variant ENST00000396618.9
LOC100506071NR_038356.1 linkuse as main transcriptn.1618-808C>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COCHENST00000396618.9 linkuse as main transcriptc.83-212G>C intron_variant 1 NM_004086.3 P1O43405-1
ENST00000555108.1 linkuse as main transcriptn.1618-808C>G intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.620
AC:
94206
AN:
151834
Hom.:
29691
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.783
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.659
Gnomad EAS
AF:
0.662
Gnomad SAS
AF:
0.809
Gnomad FIN
AF:
0.570
Gnomad MID
AF:
0.703
Gnomad NFE
AF:
0.635
Gnomad OTH
AF:
0.657
GnomAD4 exome
AF:
0.656
AC:
285389
AN:
434892
Hom.:
94728
Cov.:
5
AF XY:
0.664
AC XY:
151506
AN XY:
228210
show subpopulations
Gnomad4 AFR exome
AF:
0.525
Gnomad4 AMR exome
AF:
0.754
Gnomad4 ASJ exome
AF:
0.669
Gnomad4 EAS exome
AF:
0.651
Gnomad4 SAS exome
AF:
0.800
Gnomad4 FIN exome
AF:
0.593
Gnomad4 NFE exome
AF:
0.639
Gnomad4 OTH exome
AF:
0.654
GnomAD4 genome
AF:
0.620
AC:
94264
AN:
151952
Hom.:
29707
Cov.:
31
AF XY:
0.624
AC XY:
46317
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.529
Gnomad4 AMR
AF:
0.741
Gnomad4 ASJ
AF:
0.659
Gnomad4 EAS
AF:
0.662
Gnomad4 SAS
AF:
0.810
Gnomad4 FIN
AF:
0.570
Gnomad4 NFE
AF:
0.635
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.617
Hom.:
3609
Bravo
AF:
0.625
Asia WGS
AF:
0.754
AC:
2622
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.6
DANN
Benign
0.35

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: rs1124181; hg19: chr14-31346566; API