Variant 19-15728555-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013939.2(OR10H2):c.512C>T(p.Ser171Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0814 in 1,613,778 control chromosomes in the GnomAD database, including 14,021 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.086 ( 1568 hom., cov: 32)

Exomes 𝑓: 0.081 ( 12453 hom. )

Consequence

OR10H2
NM_013939.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.858

Variant links:

Genes affected

OR10H2 (HGNC:8173): (olfactory receptor family 10 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]

OR10H2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.8928684E-5).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR10H2	NM_013939.2 linkuse as main transcript	c.512C>T	p.Ser171Phe	missense_variant	1/1	ENST00000305899.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR10H2	ENST00000305899.5 linkuse as main transcript	c.512C>T	p.Ser171Phe	missense_variant	1/1		NM_013939.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0860

AC:

13078

AN:

152114

Hom.:

1565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0314

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.571

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0759

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0517

Gnomad OTH

AF:

0.0833

GnomAD3 exomes

AF:

0.139

AC:

34811

AN:

251326

Hom.:

5674

AF XY:

0.126

AC XY:

17140

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.0303

Gnomad AMR exome

AF:

0.342

Gnomad ASJ exome

AF:

0.0520

Gnomad EAS exome

AF:

0.562

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.0835

Gnomad NFE exome

AF:

0.0506

Gnomad OTH exome

AF:

0.0967

GnomAD4 exome

AF:

0.0809

AC:

118246

AN:

1461546

Hom.:

12453

Cov.:

AF XY:

0.0800

AC XY:

58176

AN XY:

726978

show subpopulations

Gnomad4 AFR exome

AF:

0.0264

Gnomad4 AMR exome

AF:

0.329

Gnomad4 ASJ exome

AF:

0.0529

Gnomad4 EAS exome

AF:

0.583

Gnomad4 SAS exome

AF:

0.114

Gnomad4 FIN exome

AF:

0.0822

Gnomad4 NFE exome

AF:

0.0523

Gnomad4 OTH exome

AF:

0.0913

GnomAD4 genome

AF:

0.0860

AC:

13097

AN:

152232

Hom.:

1568

Cov.:

AF XY:

0.0932

AC XY:

6936

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0314

Gnomad4 AMR

AF:

0.229

Gnomad4 ASJ

AF:

0.0510

Gnomad4 EAS

AF:

0.571

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.0759

Gnomad4 NFE

AF:

0.0517

Gnomad4 OTH

AF:

0.0890

Alfa

AF:

0.0672

Hom.:

2396

Bravo

AF:

0.0965

TwinsUK

AF:

0.0477

AC:

177

ALSPAC

AF:

0.0610

AC:

235

ESP6500AA

AF:

0.0329

AC:

145

ESP6500EA

AF:

0.0549

AC:

472

ExAC

AF:

0.127

AC:

15356

Asia WGS

AF:

0.316

AC:

1096

AN:

3478

EpiCase

AF:

0.0464

EpiControl

AF:

0.0456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.034

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.68

FATHMM_MKL

Benign

0.049

LIST_S2

Benign

0.23

MetaRNN

Benign

0.000029

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.3

MutationTaster

Benign

1.0

PrimateAI

Benign

0.19

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.019

Sift

Benign

0.034

Sift4G

Uncertain

0.031

Polyphen

0.73

Vest4

0.076

MPC

0.60

ClinPred

0.067

GERP RS

0.98

Varity_R

0.16

gMVP

0.061

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over