rs35634161

Variant names:

• chr1-159439967-T-C
• rs35634161
• NM_012351.3:c.176T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-159439967-T-C
• chr1-159439967-T-G

Variant summary

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

The NM_012351.3(OR10J1):​c.176T>C​(p.Met59Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0176 in 1,614,140 control chromosomes in the GnomAD database, including 394 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 0.015 (52 hom., cov: 32)
  • Exomes 𝑓: 0.018 (342 hom.)
• Consequence: OR10J1 NM_012351.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.00
• Publications: 12 publications found

Genes affected

OR10J1 (HGNC:8175): (olfactory receptor family 10 subfamily J 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]

ENSG00000228560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=0.011399478).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.056 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012351.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10J1	NM_012351.3	MANE Select	c.176T>C	p.Met59Thr	missense	Exon 1 of 1	NP_036483.3
	OR10J1	NM_001363557.2		c.176T>C	p.Met59Thr	missense	Exon 5 of 5	NP_001350486.1
	OR10J1	NM_001363558.2		c.176T>C	p.Met59Thr	missense	Exon 4 of 4	NP_001350487.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10J1	ENST00000423932.6	TSL:6 MANE Select	c.176T>C	p.Met59Thr	missense	Exon 1 of 1	ENSP00000399078.4
	ENSG00000228560	ENST00000431862.1	TSL:1	n.227+28875A>G		intron	N/A
	OR10J1	ENST00000641630.1		c.209T>C	p.Met70Thr	missense	Exon 1 of 1	ENSP00000492902.1

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2352 AN: 152178 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.00263

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00969

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0105

GnomAD2 exomes AF: 0.0195 AC: 4892 AN: 251148 AF XY: 0.0193

Gnomad AFR exome AF: 0.00246

Gnomad AMR exome AF: 0.00570

Gnomad ASJ exome AF: 0.00278

Gnomad EAS exome AF: 0.0578

Gnomad FIN exome AF: 0.0418

Gnomad NFE exome AF: 0.0197

Gnomad OTH exome AF: 0.0178

GnomAD4 exome AF: 0.0178 AC: 26040 AN: 1461844 Hom.: 342 Cov.: 64 AF XY: 0.0176 AC XY: 12807 AN XY: 727218

African (AFR) AF: 0.00233 AC: 78 AN: 33478

American (AMR) AF: 0.00595 AC: 266 AN: 44710

Ashkenazi Jewish (ASJ) AF: 0.00214 AC: 56 AN: 26136

East Asian (EAS) AF: 0.0765 AC: 3038 AN: 39700

South Asian (SAS) AF: 0.0103 AC: 889 AN: 86256

European-Finnish (FIN) AF: 0.0402 AC: 2148 AN: 53420

Middle Eastern (MID) AF: 0.00433 AC: 25 AN: 5768

European-Non Finnish (NFE) AF: 0.0167 AC: 18566 AN: 1111984

Other (OTH) AF: 0.0161 AC: 974 AN: 60392

GnomAD4 genome AF: 0.0154 AC: 2351 AN: 152296 Hom.: 52 Cov.: 32 AF XY: 0.0163 AC XY: 1216 AN XY: 74454

African (AFR) AF: 0.00262 AC: 109 AN: 41570

American (AMR) AF: 0.00967 AC: 148 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.000864 AC: 3 AN: 3472

East Asian (EAS) AF: 0.0616 AC: 319 AN: 5180

South Asian (SAS) AF: 0.00932 AC: 45 AN: 4826

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1233 AN: 68016

Other (OTH) AF: 0.0109 AC: 23 AN: 2114

Alfa AF: 0.0174 Hom.: 110

Bravo AF: 0.0126

TwinsUK AF: 0.0148 AC: 55

ALSPAC AF: 0.0182 AC: 70

ESP6500AA AF: 0.00386 AC: 17

ESP6500EA AF: 0.0187 AC: 161

ExAC AF: 0.0202 AC: 2452

Asia WGS AF: 0.0210 AC: 74 AN: 3478

EpiCase AF: 0.0133

EpiControl AF: 0.0130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Benign	-0.48	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0064	T
Eigen	Uncertain	0.68
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D
MetaRNN	Benign	0.011	T
MetaSVM	Benign	-0.82	T
MutationAssessor	Pathogenic	3.4	M
PhyloP100		5.0
PrimateAI	Benign	0.23	T
REVEL	Benign	0.21
Polyphen		1.0	D
MPC		0.012
ClinPred		0.061	T
GERP RS		4.5
PromoterAI		0.040	Neutral
Varity_R		0.91
gMVP		0.090
Mutation Taster		=93/7	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: rs35634161; hg19: chr1-159409757; COSMIC: COSV71129052;