11-4475616-C-T

Position:

• chr11-4475616-C-T

Variant summary

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

The ENST00000531655.1(OR52K3P):​n.804C>T 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 0.291 in 608,732 control chromosomes in the GnomAD database, including 26,586 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 0.27 (5949 hom., cov: 32)
  • Exomes 𝑓: 0.30 (20637 hom.)
• Consequence: OR52K3P ENST00000531655.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 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
OR52K3P	ENST00000531655.1	n.804C>T		non_coding_transcript_exon_variant	1/1
	ENST00000690302.1	n.380-44047C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41358 AN: 151914 Hom.: 5938 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.279

GnomAD4 exome AF: 0.297 AC: 135712 AN: 456698 Hom.: 20637 Cov.: 4 AF XY: 0.294 AC XY: 71838 AN XY: 244172

Gnomad4 AFR exome AF: 0.180

Gnomad4 AMR exome AF: 0.322

Gnomad4 ASJ exome AF: 0.217

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.260

Gnomad4 FIN exome AF: 0.378

Gnomad4 NFE exome AF: 0.298

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.272 AC: 41397 AN: 152034 Hom.: 5949 Cov.: 32 AF XY: 0.275 AC XY: 20390 AN XY: 74280

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.278

Alfa AF: 0.294 Hom.: 14454

Bravo AF: 0.265

Asia WGS AF: 0.313 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278170; hg19: chr11-4496846;