rs764836025

Variant names:

• chr1-248295220-C-A
• NM_001004692.2:c.359G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-248295220-C-A
• chr1-248295220-C-G
• chr1-248295220-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001004692.2(OR2T12):​c.359G>T​(p.Arg120Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000000686 in 1,458,724 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R120H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: OR2T12 NM_001004692.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.25

Genes affected

OR2T12 (HGNC:19592): (olfactory receptor family 2 subfamily T member 12) 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

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2T12	NM_001004692.2	c.359G>T	p.Arg120Leu	missense_variant	Exon 3 of 3	ENST00000641276.1	NP_001004692.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2T12	ENST00000641276.1	c.359G>T	p.Arg120Leu	missense_variant	Exon 3 of 3		NM_001004692.2	ENSP00000493000.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1458724 Hom.: 0 Cov.: 72 AF XY: 0.00 AC XY: 0 AN XY: 725630

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.46
BayesDel_addAF	Uncertain	0.087	D
BayesDel_noAF	Benign	-0.11
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	T;T
Eigen	Uncertain	0.19
Eigen_PC	Benign	-0.097
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.87	.;D
M_CAP	Benign	0.0096	T
MetaRNN	Uncertain	0.69	D;D
MetaSVM	Uncertain	0.44	D
MutationAssessor	Pathogenic	3.7	H;H
PrimateAI	Benign	0.23	T
PROVEAN	Pathogenic	-6.3	.;D
REVEL	Uncertain	0.44
Sift	Uncertain	0.0010	.;D
Sift4G	Uncertain	0.0070	.;D
Polyphen		0.99	D;D
Vest4		0.33
MutPred		0.43		Loss of methylation at R120 (P = 0.0391);Loss of methylation at R120 (P = 0.0391);
MVP		0.82
MPC		1.4
ClinPred		0.99	D
GERP RS		1.6
Varity_R		0.74
gMVP		0.72

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-248458522;