rs11755182

Variant names:

• chr6-29440280-C-A
• rs11755182
• NM_013941.4:c.265C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29440280-C-A
• chr6-29440280-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 13/21 in silico tools predict 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 (276 hom., cov: 32)
  • Exomes 𝑓: 0.011 (371 hom.)
• Consequence: OR10C1 NM_013941.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 7 publications found

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]

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]

ACMG classification

Our verdict: Benign. The variant received -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	c.265C>A	p.Arg89Ser	missense_variant	Exon 1 of 1	ENST00000444197.3	NP_039229.3
OR11A1	NM_001394828.1	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	Appris	UniProt
OR10C1	ENST00000444197.3	c.265C>A	p.Arg89Ser	missense_variant	Exon 1 of 1	6	NM_013941.4	ENSP00000419119.1
OR11A1	ENST00000377149.5	c.-388-8293G>T		intron_variant	Intron 1 of 4	6	NM_001394828.1	ENSP00000366354.1
OR10C1	ENST00000622521.1	c.271C>A	p.Arg91Ser	missense_variant	Exon 1 of 1	6		ENSP00000481429.1

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5935 AN: 152132 Hom.: 276 Cov.: 32

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: 4373 AN: 247210 AF XY: 0.0157

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 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.: 35 AF XY: 0.0111 AC XY: 8041 AN XY: 727140

African (AFR) AF: 0.120 AC: 4021 AN: 33470

American (AMR) AF: 0.0211 AC: 945 AN: 44722

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: 0.000620 AC: 33 AN: 53256

Middle Eastern (MID) AF: 0.0413 AC: 238 AN: 5768

European-Non Finnish (NFE) AF: 0.00748 AC: 8322 AN: 1111980

Other (OTH) AF: 0.0189 AC: 1139 AN: 60392

GnomAD4 genome AF: 0.0391 AC: 5946 AN: 152252 Hom.: 276 Cov.: 32 AF XY: 0.0374 AC XY: 2788 AN XY: 74452

African (AFR) AF: 0.113 AC: 4700 AN: 41516

American (AMR) AF: 0.0235 AC: 360 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5172

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4822

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10622

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00844 AC: 574 AN: 68028

Other (OTH) AF: 0.0430 AC: 91 AN: 2116

Alfa AF: 0.0169 Hom.: 129

Bravo AF: 0.0448

TwinsUK AF: 0.0108 AC: 40

ALSPAC AF: 0.00856 AC: 33

ESP6500AA AF: 0.118 AC: 357

ESP6500EA AF: 0.00868 AC: 47

ExAC AF: 0.0185 AC: 2230

Asia WGS AF: 0.0240 AC: 82 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	T
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	N
MetaRNN	Benign	0.0037	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.61	N;.
PhyloP100		-0.30
PrimateAI	Benign	0.19	T
PROVEAN	Uncertain	-3.1	D;.
REVEL	Benign	0.060
Sift	Uncertain	0.011	D;.
Polyphen		0.69	P;.
MPC		0.39
ClinPred		0.011	T
GERP RS		2.4
PromoterAI		-0.0098	Neutral
Varity_R		0.24
gMVP		0.29
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11755182; hg19: chr6-29408057;