rs1376486

chr11-58189360-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005283.3(OR9Q2):c.-173+252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,066 control chromosomes in the GnomAD database, including 5,036 homozygotes. 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 0.25 (5036 hom., cov: 32)
• Consequence: OR9Q2 NM_001005283.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437

Genes affected

OR9Q2 (HGNC:15328): (olfactory receptor family 9 subfamily Q 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR9Q2	NM_001005283.3	c.-173+252C>T		intron_variant		ENST00000641291.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR9Q2	ENST00000641291.1	c.-173+252C>T		intron_variant			NM_001005283.3	P1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38451 AN: 151948 Hom.: 5034 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.253 AC: 38470 AN: 152066 Hom.: 5036 Cov.: 32 AF XY: 0.248 AC XY: 18414 AN XY: 74320

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.0763

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.208

Alfa AF: 0.256 Hom.: 10627

Bravo AF: 0.258

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.2
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376486; hg19: chr11-57956832;