NM_013941.4:c.361C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013941.4(OR10C1):c.361C>T(p.Arg121Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00975 in 1,614,030 control chromosomes in the GnomAD database, including 303 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.

Frequency

Genomes: 𝑓 0.027 ( 115 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 188 hom. )

Consequence

OR10C1
NM_013941.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.704

Publications

9 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.016771823).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10C1	NM_013941.4 link	c.361C>T	p.Arg121Cys	missense_variant	Exon 1 of 1	ENST00000444197.3	NP_039229.3	Q96KK4A0A126GV80
OR11A1	NM_001394828.1 link	c.-388-8389G>A		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.361C>T	p.Arg121Cys	missense_variant	Exon 1 of 1	6	NM_013941.4	ENSP00000419119.1	Q96KK4
OR11A1	ENST00000377149.5 link	c.-388-8389G>A		intron_variant	Intron 1 of 4	6	NM_001394828.1	ENSP00000366354.1	Q9GZK7
OR10C1	ENST00000622521.1 link	c.367C>T	p.Arg123Cys	missense_variant	Exon 1 of 1	6		ENSP00000481429.1	A0A087WY02

Frequencies

GnomAD3 genomes

AF:

0.0266

AC:

4041

AN:

152186

Hom.:

115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0756

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0157

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.0114

Gnomad SAS

AF:

0.0159

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00564

Gnomad OTH

AF:

0.0330

GnomAD2 exomes

AF:

0.0133

AC:

3288

AN:

247838

AF XY:

0.0120

show subpopulations

Gnomad AFR exome

AF:

0.0801

Gnomad AMR exome

AF:

0.0141

Gnomad ASJ exome

AF:

0.0206

Gnomad EAS exome

AF:

0.00879

Gnomad FIN exome

AF:

0.000462

Gnomad NFE exome

AF:

0.00614

Gnomad OTH exome

AF:

0.0138

GnomAD4 exome

AF:

0.00800

AC:

11694

AN:

1461726

Hom.:

188

Cov.:

AF XY:

0.00796

AC XY:

5791

AN XY:

727166

show subpopulations

African (AFR)

AF:

0.0810

AC:

2710

AN:

33468

American (AMR)

AF:

0.0156

AC:

697

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0214

AC:

558

AN:

26134

East Asian (EAS)

AF:

0.00398

AC:

158

AN:

39698

South Asian (SAS)

AF:

0.0132

AC:

1140

AN:

86256

European-Finnish (FIN)

AF:

0.000412

AC:

AN:

53344

Middle Eastern (MID)

AF:

0.0354

AC:

204

AN:

5768

European-Non Finnish (NFE)

AF:

0.00480

AC:

5339

AN:

1111940

Other (OTH)

AF:

0.0143

AC:

866

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

758

1515

2273

3030

3788

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0266

AC:

4047

AN:

152304

Hom.:

115

Cov.:

AF XY:

0.0253

AC XY:

1882

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.0756

AC:

3141

AN:

41546

American (AMR)

AF:

0.0156

AC:

239

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3472

East Asian (EAS)

AF:

0.0112

AC:

AN:

5180

South Asian (SAS)

AF:

0.0153

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0000941

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00565

AC:

384

AN:

68022

Other (OTH)

AF:

0.0326

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

199

398

597

796

995

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0147

Hom.:

101

Bravo

AF:

0.0299

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.0785

AC:

237

ESP6500EA

AF:

0.00720

AC:

ExAC

AF:

0.0137

AC:

1660

Asia WGS

AF:

0.0220

AC:

AN:

3478

EpiCase

AF:

0.00714

EpiControl

AF:

0.00788

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.087

T;.

Eigen

Benign

-0.0018

Eigen_PC

Benign

-0.10

FATHMM_MKL

Benign

0.58

MetaRNN

Benign

0.017

T;T

MetaSVM

Uncertain

-0.075

MutationAssessor

Uncertain

2.7

M;.

PhyloP100

0.70

PrimateAI

Benign

0.23

PROVEAN

Pathogenic

-7.8

D;.

REVEL

Uncertain

0.40

Sift

Uncertain

0.0070

D;.

Polyphen

0.77

P;.

MPC

1.3

ClinPred

0.041

GERP RS

3.1

PromoterAI

-0.010

Neutral

(source)

Varity_R

0.59

gMVP

0.60

Mutation Taster

=92/8

polymorphism (auto)

(source)

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

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NM_013941.4:c.361C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over