11-5552350-T-G

Variant names:

• chr11-5552350-T-G
• rs10500651
• ENST00000380259.7:n.*739+38475A>C

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+38475A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 153,936 control chromosomes in the GnomAD database, including 4,523 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 0.24 (4472 hom., cov: 32)
  • Exomes 𝑓: 0.22 (51 hom.)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ENSG00000239920 (HGNC:):

OR52H2P (HGNC:15219): (olfactory receptor family 52 subfamily H 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52H2P		n.5552350T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+38475A>C		intron_variant	Intron 5 of 7	5		ENSP00000369609.3
OR52H2P	ENST00000514607.1	n.214A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35939 AN: 151870 Hom.: 4467 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.242

GnomAD4 exome AF: 0.225 AC: 438 AN: 1948 Hom.: 51 Cov.: 0 AF XY: 0.253 AC XY: 276 AN XY: 1090

Gnomad4 AFR exome AF: 0.231

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.303

GnomAD4 genome AF: 0.237 AC: 35962 AN: 151988 Hom.: 4472 Cov.: 32 AF XY: 0.232 AC XY: 17235 AN XY: 74298

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0795

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.244

Alfa AF: 0.233 Hom.: 2204

Bravo AF: 0.237

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.6
DANN	Benign	0.65

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: rs10500651; hg19: chr11-5573580;