NM_001005487.2:c.394A>G

Variant names:

• chr1-247672648-T-C
• rs1151640
• NM_001005487.2:c.394A>G

Variant summary

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

The NM_001005487.2(OR13G1):​c.394A>G​(p.Ile132Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 1,613,520 control chromosomes in the GnomAD database, including 155,796 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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 0.37 (11792 hom., cov: 32)
  • Exomes 𝑓: 0.44 (144004 hom.)
• Consequence: OR13G1 NM_001005487.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 37 publications found

Genes affected

OR13G1 (HGNC:14999): (olfactory receptor family 13 subfamily G 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]

ENSG00000235749 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (MetaRNN=5.544733E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005487.2. 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
	OR13G1	NM_001005487.2	MANE Select	c.394A>G	p.Ile132Val	missense	Exon 2 of 2	NP_001005487.1	Q8NGZ3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR13G1	ENST00000642119.1	MANE Select	c.394A>G	p.Ile132Val	missense	Exon 2 of 2	ENSP00000493110.1	Q8NGZ3
	ENSG00000235749	ENST00000449298.2	TSL:1	n.685+32219T>C		intron	N/A
	ENSG00000235749	ENST00000746711.1		n.432T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56268 AN: 151792 Hom.: 11781 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.368

GnomAD2 exomes AF: 0.458 AC: 114803 AN: 250916 AF XY: 0.453

Gnomad AFR exome AF: 0.159

Gnomad AMR exome AF: 0.666

Gnomad ASJ exome AF: 0.421

Gnomad EAS exome AF: 0.599

Gnomad FIN exome AF: 0.410

Gnomad NFE exome AF: 0.433

Gnomad OTH exome AF: 0.445

GnomAD4 exome AF: 0.438 AC: 640088 AN: 1461612 Hom.: 144004 Cov.: 58 AF XY: 0.438 AC XY: 318168 AN XY: 727092

African (AFR) AF: 0.159 AC: 5306 AN: 33470

American (AMR) AF: 0.653 AC: 29175 AN: 44676

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 11049 AN: 26132

East Asian (EAS) AF: 0.621 AC: 24664 AN: 39700

South Asian (SAS) AF: 0.435 AC: 37513 AN: 86252

European-Finnish (FIN) AF: 0.414 AC: 22138 AN: 53418

Middle Eastern (MID) AF: 0.362 AC: 2086 AN: 5766

European-Non Finnish (NFE) AF: 0.434 AC: 482605 AN: 1111816

Other (OTH) AF: 0.423 AC: 25552 AN: 60382

GnomAD4 genome AF: 0.371 AC: 56291 AN: 151908 Hom.: 11792 Cov.: 32 AF XY: 0.374 AC XY: 27767 AN XY: 74240

African (AFR) AF: 0.165 AC: 6823 AN: 41430

American (AMR) AF: 0.540 AC: 8242 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3010 AN: 5144

South Asian (SAS) AF: 0.432 AC: 2081 AN: 4812

European-Finnish (FIN) AF: 0.400 AC: 4230 AN: 10566

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29250 AN: 67908

Other (OTH) AF: 0.373 AC: 788 AN: 2112

Alfa AF: 0.414 Hom.: 41173

Bravo AF: 0.376

TwinsUK AF: 0.436 AC: 1616

ALSPAC AF: 0.449 AC: 1729

ESP6500AA AF: 0.168 AC: 739

ESP6500EA AF: 0.425 AC: 3654

ExAC AF: 0.445 AC: 54006

Asia WGS AF: 0.507 AC: 1758 AN: 3478

EpiCase AF: 0.420

EpiControl AF: 0.425

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.79	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.5
DANN	Benign	0.74
DEOGEN2	Benign	0.0060	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.053	N
LIST_S2	Benign	0.13	T
MetaRNN	Benign	0.0000055	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.1	L
PhyloP100		0.15
PrimateAI	Benign	0.20	T
PROVEAN	Benign	-0.32	N
REVEL	Benign	0.022
Sift	Benign	0.21	T
Sift4G	Benign	0.31	T
Polyphen		0.0020	B
Vest4		0.017
MPC		0.12
ClinPred		0.0082	T
GERP RS		-3.4
Varity_R		0.10
gMVP		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1151640; hg19: chr1-247835950; COSMIC: COSV62943381; COSMIC: COSV62943381;