NM_013941.4:c.163C>T

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_013941.4(OR10C1):c.163C>T(p.Gln55*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00871 in 1,613,722 control chromosomes in the GnomAD database, including 274 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.025 ( 115 hom., cov: 32)

Exomes 𝑓: 0.0070 ( 159 hom. )

Consequence

OR10C1
NM_013941.4 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.70

Publications

13 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013941.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10C1	NM_013941.4	MANE Select	c.163C>T	p.Gln55*	stop_gained	Exon 1 of 1	NP_039229.3
	OR11A1	NM_001394828.1	MANE Select	c.-388-8191G>A		intron	N/A	NP_001381757.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
OR10C1	ENST00000444197.3	TSL:6 MANE Select	c.163C>T	p.Gln55*	stop_gained	Exon 1 of 1	ENSP00000419119.1
OR11A1	ENST00000377149.5	TSL:6 MANE Select	c.-388-8191G>A		intron	N/A	ENSP00000366354.1
OR10C1	ENST00000622521.1	TSL:6	c.169C>T	p.Gln57*	stop_gained	Exon 1 of 1	ENSP00000481429.1

Frequencies

GnomAD3 genomes

AF:

0.0253

AC:

3852

AN:

152150

Hom.:

114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0744

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0156

Gnomad ASJ

AF:

0.0222

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00551

Gnomad OTH

AF:

0.0330

GnomAD2 exomes

AF:

0.0109

AC:

2704

AN:

247104

AF XY:

0.00931

show subpopulations

Gnomad AFR exome

AF:

0.0804

Gnomad AMR exome

AF:

0.0140

Gnomad ASJ exome

AF:

0.0206

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000462

Gnomad NFE exome

AF:

0.00591

Gnomad OTH exome

AF:

0.0127

GnomAD4 exome

AF:

0.00697

AC:

10193

AN:

1461454

Hom.:

159

Cov.:

AF XY:

0.00667

AC XY:

4849

AN XY:

727042

show subpopulations

African (AFR)

AF:

0.0798

AC:

2671

AN:

33470

American (AMR)

AF:

0.0154

AC:

687

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0213

AC:

558

AN:

26136

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39700

South Asian (SAS)

AF:

0.00174

AC:

150

AN:

86258

European-Finnish (FIN)

AF:

0.000434

AC:

AN:

53016

Middle Eastern (MID)

AF:

0.0324

AC:

187

AN:

5768

European-Non Finnish (NFE)

AF:

0.00466

AC:

5178

AN:

1111992

Other (OTH)

AF:

0.0122

AC:

737

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

623

1246

1868

2491

3114

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

232

464

696

928

1160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0254

AC:

3861

AN:

152268

Hom.:

115

Cov.:

AF XY:

0.0240

AC XY:

1785

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.0744

AC:

3090

AN:

41532

American (AMR)

AF:

0.0155

AC:

237

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5174

South Asian (SAS)

AF:

0.00145

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0000941

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00551

AC:

375

AN:

68026

Other (OTH)

AF:

0.0327

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

184

369

553

738

922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0136

Hom.:

Bravo

AF:

0.0293

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.0778

AC:

235

ESP6500EA

AF:

0.00720

AC:

ExAC

AF:

0.0113

AC:

1355

Asia WGS

AF:

0.00751

AC:

AN:

3478

EpiCase

AF:

0.00687

EpiControl

AF:

0.00723

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.22

BayesDel_noAF

Pathogenic

0.60

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Uncertain

0.84

PhyloP100

2.7

GERP RS

3.7

PromoterAI

0.0053

Neutral

(source)

Mutation Taster

=172/28

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over