rs11603357

chr11-4431820-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000527287.1(OR52P2P):n.458G>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 0.0564 in 153,044 control chromosomes in the GnomAD database, including 326 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 0.057 (326 hom., cov: 33)
  • Exomes 𝑓: 0.038 (0 hom.)
• Consequence: OR52P2P ENST00000527287.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

OR52P2P (HGNC:15233): (olfactory receptor family 52 subfamily P 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR52P2P	ENST00000527287.1	n.458G>A		non_coding_transcript_exon_variant	1/1
	ENST00000690302.1	n.379+37655C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8590 AN: 152182 Hom.: 324 Cov.: 33

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0512

GnomAD4 exome AF: 0.0375 AC: 28 AN: 746 Hom.: 0 Cov.: 0 AF XY: 0.0378 AC XY: 17 AN XY: 450

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0383

Gnomad4 NFE exome AF: 0.0316

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0565 AC: 8606 AN: 152298 Hom.: 326 Cov.: 33 AF XY: 0.0564 AC XY: 4199 AN XY: 74466

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0681 Hom.: 81

Bravo AF: 0.0602

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	17
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603357; hg19: chr11-4453050;