Genetic Variant OR52P2P:n.458G>A (chr11-4431820-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

Publications

1 publications found

Variant links:

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]

OR52P2P links:

ENSG00000291144 (HGNC:):

ENSG00000291144 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR52P2P		n.4431820C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR52P2P	ENST00000527287.1 link	n.458G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291144	ENST00000641797.5 link	n.387-37547C>T	intron_variant	Intron 1 of 2
ENSG00000291144	ENST00000685350.2 link	n.392-37547C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0564

AC:

8590

AN:

152182

Hom.:

324

Cov.:

show subpopulations

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:

AN:

746

Hom.:

Cov.:

AF XY:

0.0378

AC XY:

AN XY:

450

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0383

AC:

AN:

522

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0316

AC:

AN:

190

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0565

AC:

8606

AN:

152298

Hom.:

326

Cov.:

AF XY:

0.0564

AC XY:

4199

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0339

AC:

1409

AN:

41584

American (AMR)

AF:

0.113

AC:

1721

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0654

AC:

227

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5178

South Asian (SAS)

AF:

0.0565

AC:

273

AN:

4830

European-Finnish (FIN)

AF:

0.0446

AC:

474

AN:

10620

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0640

AC:

4355

AN:

68006

Other (OTH)

AF:

0.0507

AC:

107

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

410

820

1230

1640

2050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0674

Hom.:

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

(source)

DANN

Benign

0.84

PhyloP100

-0.13

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over