dbSNP rs9633905: OR52K3P:n.571C>A (chr11-4475383-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0800

Publications

5 publications found

Variant links:

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]

OR52K3P links:

ENSG00000291144 (HGNC:):

ENSG00000291144 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
OR52K3P		n.4475383C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR52K3P	ENST00000531655.1 link	n.571C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291144	ENST00000641797.5 link	n.1185C>A	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291144	ENST00000690343.2 link	n.1020C>A	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39516

AN:

152018

Hom.:

5637

Cov.:

show subpopulations

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.:

AF XY:

0.303

AC XY:

211625

AN XY:

697792

show subpopulations

African (AFR)

AF:

0.130

AC:

4193

AN:

32152

American (AMR)

AF:

0.322

AC:

14358

AN:

44546

Ashkenazi Jewish (ASJ)

AF:

0.225

AC:

5767

AN:

25626

East Asian (EAS)

AF:

0.348

AC:

13711

AN:

39372

South Asian (SAS)

AF:

0.259

AC:

21979

AN:

84714

European-Finnish (FIN)

AF:

0.385

AC:

20523

AN:

53352

Middle Eastern (MID)

AF:

0.214

AC:

1212

AN:

5654

European-Non Finnish (NFE)

AF:

0.310

AC:

326459

AN:

1051570

Other (OTH)

AF:

0.289

AC:

16809

AN:

58110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

15159

30318

45477

60636

75795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10482

20964

31446

41928

52410

<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:

0.260

AC:

39539

AN:

152136

Hom.:

5647

Cov.:

AF XY:

0.263

AC XY:

19543

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.142

AC:

5884

AN:

41522

American (AMR)

AF:

0.278

AC:

4245

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

796

AN:

3466

East Asian (EAS)

AF:

0.366

AC:

1891

AN:

5166

South Asian (SAS)

AF:

0.247

AC:

1192

AN:

4818

European-Finnish (FIN)

AF:

0.390

AC:

4120

AN:

10576

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.301

AC:

20488

AN:

67982

Other (OTH)

AF:

0.268

AC:

567

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1464

2928

4391

5855

7319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.270

Hom.:

1133

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

(source)

DANN

Benign

0.73

PhyloP100

-0.080

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