11-58027924-A-G

Variant summary

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

The NM_001005212.4(OR9Q1):c.-93+3820A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,112 control chromosomes in the GnomAD database, including 8,886 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 0.33 (8886 hom., cov: 32)
• Consequence: OR9Q1 NM_001005212.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

OR9Q1 (HGNC:14724): (olfactory receptor family 9 subfamily Q member 1) 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR9Q1	NM_001005212.4	c.-93+3820A>G		intron_variant		ENST00000335397.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR9Q1	ENST00000335397.3	c.-93+3820A>G		intron_variant			NM_001005212.4	P1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50613 AN: 151994 Hom.: 8863 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.333 AC: 50679 AN: 152112 Hom.: 8886 Cov.: 32 AF XY: 0.341 AC XY: 25345 AN XY: 74362

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.304

Alfa AF: 0.304 Hom.: 1101

Bravo AF: 0.321

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.5
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: rs921134; hg19: chr11-57795396;