rs1770043

Variant names:

• chr1-248488626-A-C
• rs1770043
• NM_001004697.2:c.38A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-248488626-A-C
• chr1-248488626-A-G
• chr1-248488626-A-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000641363.1(OR2T5):​c.38A>C​(p.Lys13Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. 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. K13R) has been classified as Benign.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 7)
  • Exomes 𝑓: 8.0e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2T5 ENST00000641363.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 15 publications found

Genes affected

OR2T5 (HGNC:15017): (olfactory receptor family 2 subfamily T member 5) 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]

ENSG00000229255 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.050172508).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641363.1. 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
	OR2T5	NM_001004697.2	MANE Select	c.38A>C	p.Lys13Thr	missense	Exon 1 of 1	NP_001004697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T5	ENST00000641363.1	MANE Select	c.38A>C	p.Lys13Thr	missense	Exon 1 of 1	ENSP00000493066.1
	ENSG00000229255	ENST00000450847.2	TSL:2	n.279-3142T>G		intron	N/A
	ENSG00000229255	ENST00000825060.1		n.326-3142T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 51792 Hom.: 0 Cov.: 7

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.05e-7 AC: 1 AN: 1242626 Hom.: 0 Cov.: 20 AF XY: 0.00000161 AC XY: 1 AN XY: 622816

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 19312

American (AMR) AF: 0.00 AC: 0 AN: 37636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22564

East Asian (EAS) AF: 0.00 AC: 0 AN: 35164

South Asian (SAS) AF: 0.00 AC: 0 AN: 74868

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 48172

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5134

European-Non Finnish (NFE) AF: 0.00000105 AC: 1 AN: 948884

Other (OTH) AF: 0.00 AC: 0 AN: 50892

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 51792 Hom.: 0 Cov.: 7 AF XY: 0.00 AC XY: 0 AN XY: 25074

African (AFR) AF: 0.00 AC: 0 AN: 3640

American (AMR) AF: 0.00 AC: 0 AN: 5582

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1564

East Asian (EAS) AF: 0.00 AC: 0 AN: 1272

South Asian (SAS) AF: 0.00 AC: 0 AN: 790

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 60

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 33074

Other (OTH) AF: 0.00 AC: 0 AN: 728

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.40
DEOGEN2	Benign	0.0013	T
Eigen	Benign	-1.8
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0084	N
M_CAP	Benign	0.00032	T
MetaRNN	Benign	0.050	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-1.8	N
PhyloP100		-1.2
PrimateAI	Benign	0.19	T
Polyphen		0.0010	B
MutPred		0.50		Gain of catalytic residue at K13 (P = 0.0243)
ClinPred		0.052	T
GERP RS		-1.3
PromoterAI		0.015	Neutral
Varity_R		0.033
gMVP		0.10
Mutation Taster		=99/1	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: rs1770043; hg19: chr1-248651927;