chr11-58189360-C-T

Variant names:

• chr11-58189360-C-T
• rs1376486
• NM_001005283.3:c.-173+252C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR9Q2	NM_001005283.3	c.-173+252C>T		intron_variant	Intron 1 of 1	ENST00000641291.1	NP_001005283.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR9Q2	ENST00000641291.1	c.-173+252C>T		intron_variant	Intron 1 of 1		NM_001005283.3	ENSP00000492924.1

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

African (AFR) AF: 0.276 AC: 11458 AN: 41454

American (AMR) AF: 0.261 AC: 3983 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.0763 AC: 395 AN: 5178

South Asian (SAS) AF: 0.154 AC: 743 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10580

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18138 AN: 67972

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.262 Hom.: 22610

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
PhyloP100		0.44
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1376486; hg19: chr11-57956832;