11-17553506-G-T

Variant names:

• chr11-17553506-G-T
• rs876657556
• NM_001292063.2:c.527G>T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001292063.2(OTOG):​c.527G>T​(p.Ser176Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OTOG NM_001292063.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

OTOG (HGNC:8516): (otogelin) The protein encoded by this gene is a component of the acellular membranes of the inner ear. Disruption of the orthologous mouse gene shows that it plays a role in auditory and vestibular functions. It is involved in fibrillar network organization, the anchoring of otoconial membranes and cupulae to the neuroepithelia, and likely in sound stimulation resistance. Mutations in this gene cause autosomal recessive nonsyndromic deafness, type 18B. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2855118).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTOG	NM_001292063.2	c.527G>T	p.Ser176Ile	missense_variant	Exon 6 of 56	ENST00000399397.6	NP_001278992.1
OTOG	NM_001277269.2	c.563G>T	p.Ser188Ile	missense_variant	Exon 5 of 55		NP_001264198.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTOG	ENST00000399397.6	c.527G>T	p.Ser176Ile	missense_variant	Exon 6 of 56	5	NM_001292063.2	ENSP00000382329.2
OTOG	ENST00000399391.7	c.563G>T	p.Ser188Ile	missense_variant	Exon 5 of 55	5		ENSP00000382323.2
OTOG	ENST00000498332.5	n.433G>T		non_coding_transcript_exon_variant	Exon 5 of 16	5
OTOG	ENST00000428619.1	c.*62G>T		downstream_gene_variant		3		ENSP00000399057.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1289924 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 624430

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.48
CADD	Benign	20
DANN	Benign	0.97
DEOGEN2	Benign	0.21	T;.
Eigen	Benign	0.11
Eigen_PC	Benign	0.071
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.61	T;T
M_CAP	Benign	0.059	D
MetaRNN	Benign	0.29	T;T
MetaSVM	Benign	-0.51	T
MutationAssessor	Uncertain	2.5	M;.
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-2.2	N;.
REVEL	Uncertain	0.36
Sift	Benign	0.056	T;.
Sift4G	Uncertain	0.0020	D;D
Vest4		0.12
MutPred		0.67		Loss of disorder (P = 0.005);.;
MVP		0.52
ClinPred		0.23	T
GERP RS		2.3
Varity_R		0.099
gMVP		0.42

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: rs876657556; hg19: chr11-17575053;