Variant 14-19713526-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001197287.2(OR11H2):c.358A>G(p.Thr120Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000029 ( 0 hom., cov: 21)

Exomes 𝑓: 0.000072 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

OR11H2
NM_001197287.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -3.08

Variant links:

Genes affected

OR11H2 (HGNC:14716): (olfactory receptor family 11 subfamily H member 2) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR11H2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.034110695).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR11H2	NM_001197287.2 linkuse as main transcript	c.358A>G	p.Thr120Ala	missense_variant	1/1	ENST00000556246.3	NP_001184216.2	Q8NH07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR11H2	ENST00000556246.3 linkuse as main transcript	c.358A>G	p.Thr120Ala	missense_variant	1/1	6	NM_001197287.2	ENSP00000485150.2		A0A2C9F2Y1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

138122

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000266

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000479

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000720

AC:

AN:

97276

Hom.:

AF XY:

0.000100

AC XY:

AN XY:

50004

show subpopulations

Gnomad AFR exome

AF:

0.00

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:

0.0000868

Gnomad NFE exome

AF:

0.000125

Gnomad OTH exome

AF:

0.000369

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000725

AC:

102

AN:

1407318

Hom.:

Cov.:

AF XY:

0.0000570

AC XY:

AN XY:

701912

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000229

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000188

Gnomad4 NFE exome

AF:

0.0000835

Gnomad4 OTH exome

AF:

0.000188

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000290

AC:

AN:

138122

Hom.:

Cov.:

AF XY:

0.0000299

AC XY:

AN XY:

66984

show subpopulations

Gnomad4 AFR

AF:

0.0000266

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000479

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000967

Hom.:

ExAC

AF:

0.0000197

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 19, 2022

The c.391A>G (p.T131A) alteration is located in exon 2 (coding exon 1) of the OR11H2 gene. This alteration results from a A to G substitution at nucleotide position 391, causing the threonine (T) at amino acid position 131 to be replaced by an alanine (A). 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

0.060

BayesDel_addAF

Benign

-0.086

BayesDel_noAF

Benign

-0.36

CADD

Benign

0.11

DANN

Benign

0.39

DEOGEN2

Benign

0.0059

T;.

FATHMM_MKL

Benign

0.0025

LIST_S2

Benign

0.69

T;T

MetaRNN

Benign

0.034

T;T

MutationAssessor

Benign

-1.2

N;.

PrimateAI

Benign

0.23

MVP

0.030

GERP RS

-2.1

Varity_R

0.043

gMVP

0.046

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over