11-58027924-A-G

Variant names:

• chr11-58027924-A-G
• rs921134
• NM_001005212.4:c.-93+3820A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005212.4. 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
	OR9Q1	NM_001005212.4	MANE Select	c.-93+3820A>G		intron	N/A	NP_001005212.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR9Q1	ENST00000335397.3	TSL:6 MANE Select	c.-93+3820A>G		intron	N/A	ENSP00000334934.3

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

African (AFR) AF: 0.340 AC: 14135 AN: 41514

American (AMR) AF: 0.299 AC: 4573 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 953 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3538 AN: 5146

South Asian (SAS) AF: 0.448 AC: 2162 AN: 4822

European-Finnish (FIN) AF: 0.430 AC: 4553 AN: 10584

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19883 AN: 67976

Other (OTH) AF: 0.304 AC: 641 AN: 2106

Alfa AF: 0.306 Hom.: 1150

Bravo AF: 0.321

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.50
PhyloP100		-0.10
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs921134; hg19: chr11-57795396;