8-132024507-C-T

Variant summary

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

The NM_001080399.3(OC90):​c.1408G>A​(p.Gly470Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000701 in 1,426,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

OC90
NM_001080399.3 missense

Scores

2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.98
Variant links:
Genes affected
OC90 (HGNC:8100): (otoconin 90) Predicted to enable calcium ion binding activity and structural molecule activity. Predicted to be involved in otolith mineralization. Predicted to be located in extracellular region. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

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=0.12664166).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OC90NM_001080399.3 linkc.1408G>A p.Gly470Arg missense_variant Exon 14 of 14 ENST00000254627.4 NP_001073868.2 Q02509-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OC90ENST00000254627.4 linkc.1408G>A p.Gly470Arg missense_variant Exon 14 of 14 2 NM_001080399.3 ENSP00000254627.3 Q02509-1
ENSG00000258417ENST00000262283.5 linkc.2044G>A p.Gly682Arg missense_variant Exon 18 of 18 5 ENSP00000262283.5 I6L893

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000438
AC:
1
AN:
228222
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
123678
show subpopulations
Gnomad AFR exome
AF:
0.0000667
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS 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:
7.01e-7
AC:
1
AN:
1426620
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
705194
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:
0.0000121
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.0000151

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 05, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1408G>A (p.G470R) alteration is located in exon 14 (coding exon 13) of the OC90 gene. This alteration results from a G to A substitution at nucleotide position 1408, causing the glycine (G) at amino acid position 470 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.56
CADD
Benign
13
DANN
Uncertain
1.0
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.062
N
LIST_S2
Benign
0.52
T;T
M_CAP
Benign
0.033
D
MetaRNN
Benign
0.13
T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.36
T
PROVEAN
Benign
-2.0
N;N
REVEL
Benign
0.095
Sift
Uncertain
0.0080
D;D
Sift4G
Benign
0.22
T;T
Vest4
0.23
MVP
0.39
MPC
0.0043
ClinPred
0.17
T
GERP RS
5.0
Varity_R
0.068
gMVP
0.31

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: rs927814356; hg19: chr8-133036754; COSMIC: COSV51845687; API