chr6-29440198-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_013941.4(OR10C1):c.183C>T(p.Phe61Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 1,613,834 control chromosomes in the GnomAD database, including 646 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 0.039 ( 275 hom., cov: 32)

Exomes 𝑓: 0.011 ( 371 hom. )

Consequence

OR10C1
NM_013941.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.516

Publications

5 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP7

Synonymous conserved (PhyloP=0.516 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10C1	NM_013941.4 link	c.183C>T	p.Phe61Phe	synonymous_variant	Exon 1 of 1	ENST00000444197.3	NP_039229.3
OR11A1	NM_001394828.1 link	c.-388-8211G>A		intron_variant	Intron 1 of 4	ENST00000377149.5	NP_001381757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
OR10C1	ENST00000444197.3 link	c.183C>T	p.Phe61Phe	synonymous_variant	Exon 1 of 1	6	NM_013941.4	ENSP00000419119.1
OR11A1	ENST00000377149.5 link	c.-388-8211G>A		intron_variant	Intron 1 of 4	6	NM_001394828.1	ENSP00000366354.1
OR10C1	ENST00000622521.1 link	c.189C>T	p.Phe63Phe	synonymous_variant	Exon 1 of 1	6		ENSP00000481429.1

Frequencies

GnomAD3 genomes

AF:

0.0390

AC:

5932

AN:

152160

Hom.:

275

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

GnomAD2 exomes

AF:

0.0177

AC:

4379

AN:

247050

AF XY:

0.0157

show subpopulations

Gnomad AFR exome

AF:

0.120

Gnomad AMR exome

AF:

0.0194

Gnomad ASJ exome

AF:

0.0206

Gnomad EAS exome

AF:

0.00875

Gnomad FIN exome

AF:

0.000693

Gnomad NFE exome

AF:

0.00879

Gnomad OTH exome

AF:

0.0171

GnomAD4 exome

AF:

0.0113

AC:

16575

AN:

1461556

Hom.:

371

Cov.:

AF XY:

0.0111

AC XY:

8043

AN XY:

727090

show subpopulations

African (AFR)

AF:

0.120

AC:

4023

AN:

33474

American (AMR)

AF:

0.0211

AC:

945

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0214

AC:

559

AN:

26136

East Asian (EAS)

AF:

0.00398

AC:

158

AN:

39700

South Asian (SAS)

AF:

0.0134

AC:

1158

AN:

86258

European-Finnish (FIN)

AF:

0.000602

AC:

AN:

53120

Middle Eastern (MID)

AF:

0.0413

AC:

238

AN:

5768

European-Non Finnish (NFE)

AF:

0.00748

AC:

8323

AN:

1111984

Other (OTH)

AF:

0.0189

AC:

1139

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

1024

2048

3073

4097

5121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

380

760

1140

1520

1900

<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:

0.0390

AC:

5943

AN:

152278

Hom.:

275

Cov.:

AF XY:

0.0374

AC XY:

2787

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.113

AC:

4697

AN:

41542

American (AMR)

AF:

0.0235

AC:

360

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0222

AC:

AN:

3472

East Asian (EAS)

AF:

0.0112

AC:

AN:

5182

South Asian (SAS)

AF:

0.0166

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000188

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00844

AC:

574

AN:

68022

Other (OTH)

AF:

0.0431

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

273

545

818

1090

1363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0214

Hom.:

394

Bravo

AF:

0.0448

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

BayesDel_noAF

Benign

-0.52

CADD

Benign

6.8

(source)

DANN

Benign

0.61

PhyloP100

0.52

PromoterAI

-0.044

Neutral

(source)

Mutation Taster

=100/0

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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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