rs79869455

Variant names:

• chr1-158420751-A-C
• rs79869455
• NM_001004476.2:c.116T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-158420751-A-C
• chr1-158420751-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001004476.2(OR10K2):​c.116T>G​(p.Leu39Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00157 in 1,613,768 control chromosomes in the GnomAD database, including 41 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 0.0081 (18 hom., cov: 31)
  • Exomes 𝑓: 0.00089 (23 hom.)
• Consequence: OR10K2 NM_001004476.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.02
• Publications: 2 publications found

Genes affected

OR10K2 (HGNC:14826): (olfactory receptor family 10 subfamily K member 2) 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=0.0049262643).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00812 (1236/152176) while in subpopulation AFR AF = 0.0286 (1186/41536). AF 95% confidence interval is 0.0272. There are 18 homozygotes in GnomAd4. There are 548 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004476.2. 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
	OR10K2	NM_001004476.2	MANE Select	c.116T>G	p.Leu39Arg	missense	Exon 2 of 2	NP_001004476.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10K2	ENST00000641042.1	MANE Select	c.116T>G	p.Leu39Arg	missense	Exon 2 of 2	ENSP00000493297.1

Frequencies

GnomAD3 genomes AF: 0.00812 AC: 1234 AN: 152058 Hom.: 18 Cov.: 31

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00230

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00479

GnomAD2 exomes AF: 0.00212 AC: 532 AN: 251120 AF XY: 0.00151

Gnomad AFR exome AF: 0.0292

Gnomad AMR exome AF: 0.00133

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000352

Gnomad OTH exome AF: 0.000978

GnomAD4 exome AF: 0.000893 AC: 1305 AN: 1461592 Hom.: 23 Cov.: 33 AF XY: 0.000761 AC XY: 553 AN XY: 727098

African (AFR) AF: 0.0322 AC: 1077 AN: 33452

American (AMR) AF: 0.00125 AC: 56 AN: 44648

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26126

East Asian (EAS) AF: 0.00 AC: 0 AN: 39682

South Asian (SAS) AF: 0.0000812 AC: 7 AN: 86254

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00295 AC: 17 AN: 5764

European-Non Finnish (NFE) AF: 0.0000117 AC: 13 AN: 1111872

Other (OTH) AF: 0.00224 AC: 135 AN: 60378

GnomAD4 genome AF: 0.00812 AC: 1236 AN: 152176 Hom.: 18 Cov.: 31 AF XY: 0.00737 AC XY: 548 AN XY: 74402

African (AFR) AF: 0.0286 AC: 1186 AN: 41536

American (AMR) AF: 0.00229 AC: 35 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 67980

Other (OTH) AF: 0.00474 AC: 10 AN: 2110

Alfa AF: 0.00530 Hom.: 0

Bravo AF: 0.00916

ESP6500AA AF: 0.0259 AC: 114

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.00238 AC: 289

EpiCase AF: 0.000164

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.44
BayesDel_addAF	Benign	-0.44	T
BayesDel_noAF	Benign	-0.38
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	T
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Benign	0.63	D
LIST_S2	Uncertain	0.88	D
MetaRNN	Benign	0.0049	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Pathogenic	3.9	H
PhyloP100		4.0
PrimateAI	Benign	0.29	T
PROVEAN	Pathogenic	-5.4	D
REVEL	Benign	0.12
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.81
MVP		0.63
MPC		0.032
ClinPred		0.093	T
GERP RS		4.1
Varity_R		0.98
gMVP		0.25
Mutation Taster		=85/15	polymorphism

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: rs79869455; hg19: chr1-158390541;