rs1770063

chr1-248449969-A-Gchr1-248449969-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001004136.2(OR2T2):c.-23+577A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (3047 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: OR2T2 NM_001004136.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

OR2T2 (HGNC:14725): (olfactory receptor family 2 subfamily T member 2) 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2T2	NM_001004136.2	c.-23+577A>G		intron_variant		ENST00000641925.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2T2	ENST00000641925.2	c.-23+577A>G		intron_variant			NM_001004136.2	P1
OR2T2	ENST00000642130.1	c.-22-2807A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 59941 AN: 119230 Hom.: 3043 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.512

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.499

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.503 AC: 59959 AN: 119266 Hom.: 3047 Cov.: 28 AF XY: 0.503 AC XY: 29174 AN XY: 58028

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.498

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1770063; hg19: chr1-248613270; COSMIC: COSV61618430; COSMIC: COSV61618430;