rs11755182

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

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

The NM_013941.4(OR10C1):c.265C>A(p.Arg89Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 1,613,934 control chromosomes in the GnomAD database, including 647 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.039 ( 276 hom., cov: 32)

Exomes 𝑓: 0.011 ( 371 hom. )

Consequence

OR10C1
NM_013941.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.299

Variant links:

Genes affected

OR10C1 (HGNC:8165): (olfactory receptor family 10 subfamily C member 1) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]

OR10C1 links:

OR11A1 (HGNC:8176): (olfactory receptor family 11 subfamily A member 1) 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]

OR11A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0036697984).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10C1	NM_013941.4 link	c.265C>A	p.Arg89Ser	missense_variant	Exon 1 of 1	ENST00000444197.3	NP_039229.3	Q96KK4A0A126GV80
OR11A1	NM_001394828.1 link	c.-388-8293G>T		intron_variant	Intron 1 of 4	ENST00000377149.5	NP_001381757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
OR10C1	ENST00000444197.3 link	c.265C>A	p.Arg89Ser	missense_variant	Exon 1 of 1	6	NM_013941.4	ENSP00000419119.1	Q96KK4
OR11A1	ENST00000377149.5 link	c.-388-8293G>T		intron_variant	Intron 1 of 4	6	NM_001394828.1	ENSP00000366354.1	Q9GZK7
OR10C1	ENST00000622521.1 link	c.271C>A	p.Arg91Ser	missense_variant	Exon 1 of 1	6		ENSP00000481429.1	A0A087WY02

Frequencies

GnomAD3 genomes

AF:

0.0390

AC:

5935

AN:

152132

Hom.:

276

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0237

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.0114

Gnomad SAS

AF:

0.0172

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00844

Gnomad OTH

AF:

0.0435

GnomAD3 exomes

AF:

0.0177

AC:

4373

AN:

247210

Hom.:

126

AF XY:

0.0157

AC XY:

2112

AN XY:

134536

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0193

Gnomad ASJ exome

AF:

0.0206

Gnomad EAS exome

AF:

0.00880

Gnomad SAS exome

AF:

0.0142

Gnomad FIN exome

AF:

0.000694

Gnomad NFE exome

AF:

0.00878

Gnomad OTH exome

AF:

0.0171

GnomAD4 exome

AF:

0.0113

AC:

16573

AN:

1461682

Hom.:

371

Cov.:

AF XY:

0.0111

AC XY:

8041

AN XY:

727140

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0211

Gnomad4 ASJ exome

AF:

0.0214

Gnomad4 EAS exome

AF:

0.00398

Gnomad4 SAS exome

AF:

0.0134

Gnomad4 FIN exome

AF:

0.000620

Gnomad4 NFE exome

AF:

0.00748

Gnomad4 OTH exome

AF:

0.0189

GnomAD4 genome

AF:

0.0391

AC:

5946

AN:

152252

Hom.:

276

Cov.:

AF XY:

0.0374

AC XY:

2788

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.113

Gnomad4 AMR

AF:

0.0235

Gnomad4 ASJ

AF:

0.0222

Gnomad4 EAS

AF:

0.0112

Gnomad4 SAS

AF:

0.0166

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00844

Gnomad4 OTH

AF:

0.0430

Alfa

AF:

0.0124

Hom.:

Bravo

AF:

0.0448

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.118

AC:

357

ESP6500EA

AF:

0.00868

AC:

ExAC

AF:

0.0185

AC:

2230

Asia WGS

AF:

0.0240

AC:

AN:

3478

EpiCase

AF:

0.00971

EpiControl

AF:

0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.59

BayesDel_noAF

Benign

-0.52

CADD

Benign

9.5

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0068

T;.

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.86

FATHMM_MKL

Benign

0.11

MetaRNN

Benign

0.0037

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.61

N;.

PrimateAI

Benign

0.19

PROVEAN

Uncertain

-3.1

D;.

REVEL

Benign

0.060

Sift

Uncertain

0.011

D;.

Polyphen

0.69

P;.

MPC

0.39

ClinPred

0.011

GERP RS

2.4

Varity_R

0.24

gMVP

0.29

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