NM_001004697.2:c.160C>T

Variant names:

• chr1-248488748-C-T
• rs554643879
• NM_001004697.2:c.160C>T

Variant summary

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

The NM_001004697.2(OR2T5):​c.160C>T​(p.His54Tyr) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 15)
  • Exomes 𝑓: 0.00033 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2T5 NM_001004697.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -3.21
• Publications: 2 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=0.0228239).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004697.2. 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
	OR2T5	NM_001004697.2	MANE Select	c.160C>T	p.His54Tyr	missense	Exon 1 of 1	NP_001004697.1	Q6IEZ7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T5	ENST00000641363.1	MANE Select	c.160C>T	p.His54Tyr	missense	Exon 1 of 1	ENSP00000493066.1	Q6IEZ7
	ENSG00000229255	ENST00000450847.2	TSL:2	n.279-3264G>A		intron	N/A
	ENSG00000229255	ENST00000825060.1		n.326-3264G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000274 AC: 33 AN: 120636 Hom.: 0 Cov.: 15

Gnomad AFR AF: 0.000226

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: 0.000433

Gnomad OTH AF: 0.000576

GnomAD2 exomes AF: 0.0000546 AC: 13 AN: 238048 AF XY: 0.0000696

Gnomad AFR exome AF: 0.000276

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000816

Gnomad OTH exome AF: 0.000167

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000334 AC: 432 AN: 1292592 Hom.: 0 Cov.: 23 AF XY: 0.000299 AC XY: 195 AN XY: 651330

African (AFR) AF: 0.000134 AC: 3 AN: 22438

American (AMR) AF: 0.00 AC: 0 AN: 44482

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25024

East Asian (EAS) AF: 0.00 AC: 0 AN: 38314

South Asian (SAS) AF: 0.00 AC: 0 AN: 81050

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53344

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5320

European-Non Finnish (NFE) AF: 0.000413 AC: 400 AN: 968550

Other (OTH) AF: 0.000518 AC: 28 AN: 54070

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000273 AC: 33 AN: 120706 Hom.: 0 Cov.: 15 AF XY: 0.000240 AC XY: 14 AN XY: 58436

African (AFR) AF: 0.000226 AC: 5 AN: 22154

American (AMR) AF: 0.00 AC: 0 AN: 13112

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3224

East Asian (EAS) AF: 0.00 AC: 0 AN: 4332

South Asian (SAS) AF: 0.00 AC: 0 AN: 3462

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9216

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 268

European-Non Finnish (NFE) AF: 0.000433 AC: 27 AN: 62306

Other (OTH) AF: 0.000569 AC: 1 AN: 1756

Alfa AF: 0.000144 Hom.: 0

ExAC AF: 0.0000505 AC: 6

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.43	T
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.69
DEOGEN2	Benign	0.0063	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0022	N
M_CAP	Benign	0.00064	T
MetaRNN	Benign	0.023	T
MetaSVM	Benign	-0.89	T
MutationAssessor	Benign	0.68	N
PhyloP100		-3.2
PrimateAI	Benign	0.27	T
Polyphen		0.0020	B
ClinPred		0.021	T
GERP RS		-5.3
PromoterAI		0.0018	Neutral
Varity_R		0.088
gMVP		0.064
Mutation Taster		=100/0	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: rs554643879; hg19: chr1-248652049;