1-248449969-A-G

Variant names:

• chr1-248449969-A-G
• rs1770063
• NM_001004136.2:c.-23+577A>G

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004136.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T2	NM_001004136.2	MANE Select	c.-23+577A>G		intron	N/A	NP_001004136.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2T2	ENST00000641925.2	MANE Select	c.-23+577A>G		intron	N/A	ENSP00000492947.1
	OR2T2	ENST00000642130.1		c.-22-2807A>G		intron	N/A	ENSP00000493326.1

Frequencies

GnomAD3 genomes AF: 0.503 AC: 59941 AN: 119230 Hom.: 3043 Cov.: 28

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.476 AC: 11414 AN: 23978

American (AMR) AF: 0.522 AC: 6739 AN: 12918

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1517 AN: 3034

East Asian (EAS) AF: 0.567 AC: 2476 AN: 4364

South Asian (SAS) AF: 0.543 AC: 2153 AN: 3966

European-Finnish (FIN) AF: 0.503 AC: 4292 AN: 8530

Middle Eastern (MID) AF: 0.512 AC: 123 AN: 240

European-Non Finnish (NFE) AF: 0.502 AC: 29969 AN: 59676

Other (OTH) AF: 0.498 AC: 878 AN: 1762

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.15
PhyloP100		0.0

Splicing

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

Other links and lift over

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