Variant 14-18601322-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001013354.1(OR11H12):c.206G>A(p.Arg69Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00383 in 1,504,224 control chromosomes in the GnomAD database, including 1,083 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 47 hom., cov: 20)

Exomes 𝑓: 0.0040 ( 1036 hom. )

Consequence

OR11H12
NM_001013354.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.518

Variant links:

Genes affected

OR11H12 (HGNC:30738): (olfactory receptor family 11 subfamily H member 12) 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]

OR11H12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.012099922).

BP6

Variant 14-18601322-G-A is Benign according to our data. Variant chr14-18601322-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644025.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR11H12	NM_001013354.1 linkuse as main transcript	c.206G>A	p.Arg69Gln	missense_variant	1/1	ENST00000550708.2	NP_001013372.1	B2RN74

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR11H12	ENST00000550708.2 linkuse as main transcript	c.206G>A	p.Arg69Gln	missense_variant	1/1	6	NM_001013354.1	ENSP00000449002.1		B2RN74

Frequencies

GnomAD3 genomes

AF:

0.00228

AC:

304

AN:

133240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000675

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00125

Gnomad ASJ

AF:

0.000311

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000232

Gnomad FIN

AF:

0.00299

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00369

Gnomad OTH

AF:

0.00223

GnomAD3 exomes

AF:

0.00237

AC:

543

AN:

228960

Hom.:

120

AF XY:

0.00254

AC XY:

315

AN XY:

124086

show subpopulations

Gnomad AFR exome

AF:

0.000818

Gnomad AMR exome

AF:

0.000992

Gnomad ASJ exome

AF:

0.000662

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000140

Gnomad FIN exome

AF:

0.00354

Gnomad NFE exome

AF:

0.00389

Gnomad OTH exome

AF:

0.00254

GnomAD4 exome

AF:

0.00398

AC:

5463

AN:

1370906

Hom.:

1036

Cov.:

AF XY:

0.00378

AC XY:

2583

AN XY:

683012

show subpopulations

Gnomad4 AFR exome

AF:

0.000939

Gnomad4 AMR exome

AF:

0.000900

Gnomad4 ASJ exome

AF:

0.000880

Gnomad4 EAS exome

AF:

0.0000257

Gnomad4 SAS exome

AF:

0.000132

Gnomad4 FIN exome

AF:

0.00341

Gnomad4 NFE exome

AF:

0.00476

Gnomad4 OTH exome

AF:

0.00423

GnomAD4 genome

AF:

0.00229

AC:

305

AN:

133318

Hom.:

Cov.:

AF XY:

0.00232

AC XY:

151

AN XY:

64984

show subpopulations

Gnomad4 AFR

AF:

0.000673

Gnomad4 AMR

AF:

0.00125

Gnomad4 ASJ

AF:

0.000311

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000233

Gnomad4 FIN

AF:

0.00299

Gnomad4 NFE

AF:

0.00371

Gnomad4 OTH

AF:

0.00221

Alfa

AF:

0.00165

Hom.:

ESP6500AA

AF:

0.000254

AC:

ESP6500EA

AF:

0.00318

AC:

ExAC

AF:

0.00239

AC:

280

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2023

OR11H12: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.69

CADD

Benign

2.2

DANN

Benign

0.80

DEOGEN2

Benign

0.0045

Eigen

Benign

-0.99

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.0013

LIST_S2

Benign

0.76

MetaRNN

Benign

0.012

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.73

PrimateAI

Benign

0.24

PROVEAN

Benign

-1.4

REVEL

Benign

0.016

Sift

Benign

0.18

Sift4G

Benign

0.14

Polyphen

0.38

Vest4

0.055

MVP

0.17

MPC

2.1

ClinPred

0.00080

GERP RS

0.58

Varity_R

0.030

gMVP

0.020

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