1-248453100-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_001004136.2(OR2T2):c.303G>A(p.Gln101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 1,367,646 control chromosomes in the GnomAD database, including 4,138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (1183 hom., cov: 32)
  • Exomes 𝑓: 0.050 (2955 hom.)
• Consequence: OR2T2 NM_001004136.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.291

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 Benign. Variant got -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-248453100-G-A is Benign according to our data. Variant chr1-248453100-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 767776.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.291 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2T2	NM_001004136.2	c.303G>A	p.Gln101=	synonymous_variant	4/4	ENST00000641925.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2T2	ENST00000641925.2	c.303G>A	p.Gln101=	synonymous_variant	4/4		NM_001004136.2	P1
OR2T2	ENST00000642130.1	c.303G>A	p.Gln101=	synonymous_variant	3/3			P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 22341 AN: 111164 Hom.: 1180 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0446

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0873

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0656

Gnomad NFE AF: 0.0983

Gnomad OTH AF: 0.140

GnomAD4 exome AF: 0.0495 AC: 62247 AN: 1256396 Hom.: 2955 Cov.: 35 AF XY: 0.0532 AC XY: 33010 AN XY: 620420

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.0851

Gnomad4 ASJ exome AF: 0.0557

Gnomad4 EAS exome AF: 0.185

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.0291

Gnomad4 OTH exome AF: 0.0662

GnomAD4 genome AF: 0.201 AC: 22379 AN: 111250 Hom.: 1183 Cov.: 32 AF XY: 0.201 AC XY: 10938 AN XY: 54298

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0873

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.0983

Gnomad4 OTH AF: 0.139

Alfa AF: 0.273 Hom.: 128

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Aug 02, 2017

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.3
Dann	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs77680148; hg19: chr1-248616401; COSMIC: COSV61617636;