rs9633905

Positions:

• chr11-4475383-C-A

Variant summary

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

The ENST00000531655.1(OR52K3P):​n.571C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,547,232 control chromosomes in the GnomAD database, including 71,605 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 0.26 (5647 hom., cov: 33)
  • Exomes 𝑓: 0.30 (65958 hom.)
• Consequence: OR52K3P ENST00000531655.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

OR52K3P (HGNC:15224): (olfactory receptor family 52 subfamily K member 3 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52K3P	ENST00000531655.1	n.571C>A		non_coding_transcript_exon_variant	1/1
	ENST00000690302.1	n.380-44280C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39516 AN: 152018 Hom.: 5637 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.305 AC: 425011 AN: 1395096 Hom.: 65958 Cov.: 27 AF XY: 0.303 AC XY: 211625 AN XY: 697792

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.322

Gnomad4 ASJ exome AF: 0.225

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.310

Gnomad4 OTH exome AF: 0.289

GnomAD4 genome AF: 0.260 AC: 39539 AN: 152136 Hom.: 5647 Cov.: 33 AF XY: 0.263 AC XY: 19543 AN XY: 74356

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.268

Alfa AF: 0.273 Hom.: 1121

Bravo AF: 0.251

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.3
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9633905; hg19: chr11-4496613;