rs2245676

Variant names:

• chr11-58145221-T-G
• rs2245676
• NM_001005212.4:c.-14-34210T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001005212.4(OR9Q1):​c.-14-34210T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,094 control chromosomes in the GnomAD database, including 17,393 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 0.46 (17383 hom., cov: 32)
  • Exomes 𝑓: 0.53 (10 hom.)
• Consequence: OR9Q1 NM_001005212.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 3 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]

OR9I2P (HGNC:15324): (olfactory receptor family 9 subfamily I member 2 pseudogene) 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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.-14-34210T>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.-14-34210T>G		intron	N/A	ENSP00000334934.3
	OR9I2P	ENST00000427941.1	TSL:6	n.727T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69136 AN: 151906 Hom.: 17347 Cov.: 32

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.446

GnomAD4 exome AF: 0.529 AC: 37 AN: 70 Hom.: 10 Cov.: 0 AF XY: 0.540 AC XY: 27 AN XY: 50

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.531 AC: 17 AN: 32

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.433 AC: 13 AN: 30

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.455 AC: 69221 AN: 152024 Hom.: 17383 Cov.: 32 AF XY: 0.452 AC XY: 33625 AN XY: 74322

African (AFR) AF: 0.661 AC: 27403 AN: 41466

American (AMR) AF: 0.484 AC: 7401 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1471 AN: 5170

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3816 AN: 10572

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24528 AN: 67930

Other (OTH) AF: 0.440 AC: 931 AN: 2114

Alfa AF: 0.387 Hom.: 6290

Bravo AF: 0.476

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	14
DANN	Benign	0.82
PhyloP100		1.0
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: rs2245676; hg19: chr11-57912693;