rs112397726

Variant names:

• chr1-248638649-C-A
• NM_001001827.2:c.610G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-248638649-C-A
• chr1-248638649-C-G
• chr1-248638649-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001001827.2(OR2T35):​c.610G>T​(p.Val204Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/21 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. V204M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 0)
• Consequence: OR2T35 NM_001001827.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.19762033).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2T35	NM_001001827.2	c.610G>T	p.Val204Leu	missense_variant	Exon 2 of 2	ENST00000641268.1	NP_001001827.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2T35	ENST00000641268.1	c.610G>T	p.Val204Leu	missense_variant	Exon 2 of 2		NM_001001827.2	ENSP00000492995.1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.034	T;T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.033	N
LIST_S2	Benign	0.80	.;T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.20	T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	L;L
PrimateAI	Benign	0.25	T
PROVEAN	Uncertain	-2.6	.;D
REVEL	Benign	0.073
Sift	Uncertain	0.0010	.;D
Sift4G	Uncertain	0.046	.;D
Polyphen		0.92	P;P
Vest4		0.13
MutPred		0.33		Loss of sheet (P = 0.437);Loss of sheet (P = 0.437);
MVP		0.40
MPC		2.2
ClinPred		0.96	D
GERP RS		1.9
Varity_R		0.50
gMVP		0.075

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: chr1-248801950;