Genetic Variant NM_001004694.3:c.190T>C (chr1-248559302-A-G) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The NM_001004694.3(OR2T29):c.190T>C(p.Tyr64His) variant causes a missense change. In-silico tool predicts a pathogenic 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. Y64D) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 8)

Failed GnomAD Quality Control

Consequence

OR2T29
NM_001004694.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.67

Publications

0 publications found

Variant links:

Genes affected

OR2T29 (HGNC:31253): (olfactory receptor family 2 subfamily T member 29) 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]

OR2T29 links:

ENSG00000224521 (HGNC:):

ENSG00000224521 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.796

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004694.3. 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
	OR2T29	NM_001004694.3	MANE Select	c.190T>C	p.Tyr64His	missense	Exon 2 of 2	NP_001004694.2	Q8NH02

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR2T29	ENST00000641069.1	MANE Select	c.190T>C	p.Tyr64His	missense	Exon 2 of 2	ENSP00000492895.1	Q8NH02
OR2T29	ENST00000328570.6	TSL:6	c.190T>C	p.Tyr64His	missense	Exon 1 of 1	ENSP00000331774.3	Q8NH02
ENSG00000224521	ENST00000436515.2	TSL:2	n.147-3298A>G		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

55588

Hom.:

Cov.:

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

Cov.:

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

55588

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

25718

African (AFR)

AF:

0.00

AC:

AN:

22852

American (AMR)

AF:

0.00

AC:

AN:

3800

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

910

East Asian (EAS)

AF:

0.00

AC:

AN:

1576

South Asian (SAS)

AF:

0.00

AC:

AN:

1130

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3578

Middle Eastern (MID)

AF:

0.00

AC:

AN:

156

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

20750

Other (OTH)

AF:

0.00

AC:

AN:

642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.51

BayesDel_addAF

Benign

-0.059

BayesDel_noAF

Benign

-0.32

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.019

Eigen

Uncertain

0.49

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.91

LIST_S2

Uncertain

0.92

M_CAP

Benign

0.0025

MetaRNN

Pathogenic

0.80

MetaSVM

Benign

-0.63

MutationAssessor

Pathogenic

3.0

PhyloP100

4.7

PrimateAI

Benign

0.38

PROVEAN

Pathogenic

-4.5

REVEL

Benign

0.22

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.43

MutPred

0.68

Loss of stability (P = 0.1255)

MVP

0.70

MPC

4.2

ClinPred

0.99

GERP RS

2.7

PromoterAI

0.0048

Neutral

(source)

Varity_R

0.90

gMVP

0.19

Mutation Taster

=92/8

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over