rs2245676

chr11-58145221-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR9Q1	NM_001005212.4	c.-14-34210T>G		intron_variant		ENST00000335397.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR9Q1	ENST00000335397.3	c.-14-34210T>G		intron_variant			NM_001005212.4	P1
OR9I2P	ENST00000427941.1	n.727T>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.433

Gnomad4 OTH exome AF: 0.833

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

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.440

Alfa AF: 0.384 Hom.: 5520

Bravo AF: 0.476

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	14
Dann	Benign	0.82

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: rs2245676; hg19: chr11-57912693;