NM_001001827.2:c.326G>A

Variant names:

• chr1-248638933-C-T
• rs780025540
• NM_001001827.2:c.326G>A

Variant summary

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

The NM_001001827.2(OR2T35):​c.326G>A​(p.Gly109Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. G109V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2T35 NM_001001827.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 1 publications found

Genes affected

OR2T35 (HGNC:31257): (olfactory receptor family 2 subfamily T member 35) 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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001827.2. 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
	OR2T35	NM_001001827.2	MANE Select	c.326G>A	p.Gly109Glu	missense	Exon 2 of 2	NP_001001827.1	Q8NGX2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T35	ENST00000641268.1	MANE Select	c.326G>A	p.Gly109Glu	missense	Exon 2 of 2	ENSP00000492995.1	Q8NGX2
	ENSG00000229255	ENST00000450847.2	TSL:2	n.195+3733G>A		intron	N/A
	ENSG00000229255	ENST00000825060.1		n.242+3733G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 281298 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 151066

African (AFR) AF: 0.00 AC: 0 AN: 14250

American (AMR) AF: 0.00 AC: 0 AN: 16428

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6668

East Asian (EAS) AF: 0.00 AC: 0 AN: 21392

South Asian (SAS) AF: 0.00 AC: 0 AN: 40508

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1094

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 149730

Other (OTH) AF: 0.00 AC: 0 AN: 14910

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.65
BayesDel_addAF	Benign	-0.024	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.038	T
Eigen	Benign	0.16
Eigen_PC	Benign	-0.069
FATHMM_MKL	Benign	0.057	N
LIST_S2	Benign	0.74	T
M_CAP	Benign	0.00085	T
MetaRNN	Uncertain	0.55	D
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.2	M
PhyloP100		-1.3
PrimateAI	Benign	0.21	T
PROVEAN	Pathogenic	-7.5	D
REVEL	Benign	0.18
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.38
MutPred		0.58		Gain of relative solvent accessibility (P = 0.1259)
MVP		0.78
MPC		3.2
ClinPred		1.0	D
GERP RS		1.8
Varity_R		0.88
gMVP		0.28
Mutation Taster		=87/13	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: rs780025540; hg19: chr1-248802234;