NM_001004694.3:c.707A>C

Variant names:

• chr1-248558785-T-G
• rs1981235
• NM_001004694.3:c.707A>C

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001004694.3(OR2T29):​c.707A>C​(p.Glu236Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.35 (1196 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2T29 NM_001004694.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.352
• Publications: 1 publications found

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]

ENSG00000224521 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0053547025).
• BP6: Variant 1-248558785-T-G is Benign according to our data. Variant chr1-248558785-T-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2286946.Status of the report is criteria_provided_single_submitter, 1 stars.

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.707A>C	p.Glu236Ala	missense	Exon 2 of 2	NP_001004694.2	Q8NH02

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T29	ENST00000641069.1	MANE Select	c.707A>C	p.Glu236Ala	missense	Exon 2 of 2	ENSP00000492895.1	Q8NH02
	OR2T29	ENST00000328570.6	TSL:6	c.707A>C	p.Glu236Ala	missense	Exon 1 of 1	ENSP00000331774.3	Q8NH02
	ENSG00000224521	ENST00000436515.2	TSL:2	n.147-3815T>G		intron	N/A

Frequencies

GnomAD3 genomes AC: 0 AN: 0 Hom.: 0 Cov.: 0

GnomAD2 exomes AF: 0.391 AC: 2964 AN: 7590 AF XY: 0.389

Gnomad AFR exome AF: 0.325

Gnomad AMR exome AF: 0.353

Gnomad ASJ exome AF: 0.258

Gnomad EAS exome AF: 0.641

Gnomad FIN exome AF: 0.476

Gnomad NFE exome AF: 0.397

Gnomad OTH exome AF: 0.301

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.351 AC: 10540 AN: 30018 Hom.: 1196 Cov.: 0 AF XY: 0.353 AC XY: 5413 AN XY: 15346

African (AFR) AF: 0.366 AC: 636 AN: 1740

American (AMR) AF: 0.314 AC: 1026 AN: 3272

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 142 AN: 456

East Asian (EAS) AF: 0.528 AC: 1082 AN: 2048

South Asian (SAS) AF: 0.376 AC: 1358 AN: 3608

European-Finnish (FIN) AF: 0.416 AC: 288 AN: 692

Middle Eastern (MID) AF: 0.267 AC: 24 AN: 90

European-Non Finnish (NFE) AF: 0.329 AC: 5505 AN: 16744

Other (OTH) AF: 0.350 AC: 479 AN: 1368

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

Alfa AF: 0.450 Hom.: 38

ExAC AF: 0.200 AC: 6

ClinVar

ClinVar submissions

Significance: Likely benign

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	0.086
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	18
DANN	Benign	0.95
DEOGEN2	Benign	0.015	T
Eigen	Benign	-0.68
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.060	N
LIST_S2	Benign	0.45	T
M_CAP	Benign	0.0014	T
MetaRNN	Benign	0.0054	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.35
PrimateAI	Benign	0.23	T
PROVEAN	Pathogenic	-4.9	D
REVEL	Benign	0.036
Sift	Benign	0.060	T
Sift4G	Uncertain	0.047	D
Polyphen		0.087	B
Vest4		0.070
MPC		3.1
ClinPred		0.043	T
GERP RS		0.10
Varity_R		0.30
gMVP		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1981235; hg19: chr1-248722086; COSMIC: COSV60771867; COSMIC: COSV60771867;