11-58024529-C-T

Variant names:

• chr11-58024529-C-T
• rs2441952
• NM_001005212.4:c.-93+425C>T

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+425C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,000 control chromosomes in the GnomAD database, including 31,584 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 0.64 (31584 hom., cov: 32)
• Consequence: OR9Q1 NM_001005212.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 1 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]

LOC107984331 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR9Q1	NM_001005212.4	c.-93+425C>T		intron_variant	Intron 1 of 2	ENST00000335397.3	NP_001005212.1
LOC107984331	XR_001748218.1	n.-110G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR9Q1	ENST00000335397.3	c.-93+425C>T		intron_variant	Intron 1 of 2	6	NM_001005212.4	ENSP00000334934.3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97321 AN: 151882 Hom.: 31554 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.641 AC: 97402 AN: 152000 Hom.: 31584 Cov.: 32 AF XY: 0.642 AC XY: 47724 AN XY: 74290

African (AFR) AF: 0.571 AC: 23659 AN: 41412

American (AMR) AF: 0.620 AC: 9462 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3891 AN: 5168

South Asian (SAS) AF: 0.791 AC: 3810 AN: 4818

European-Finnish (FIN) AF: 0.707 AC: 7483 AN: 10580

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45231 AN: 67968

Other (OTH) AF: 0.634 AC: 1338 AN: 2112

Alfa AF: 0.629 Hom.: 4518

Bravo AF: 0.628

Asia WGS AF: 0.748 AC: 2601 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	3.4
DANN	Benign	0.90
PhyloP100		0.13
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: rs2441952; hg19: chr11-57792001;