Genetic Variant ENST00000531655.1:n.804C>T (chr11-4475616-C-T) – 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88

Publications

12 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=-0.79).

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 rank	MANE	Protein	UniProt
OR52K3P		n.4475616C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR52K3P	ENST00000531655.1 link	n.804C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291144	ENST00000641797.5 link	n.1418C>T	non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291144	ENST00000690343.2 link	n.1253C>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

41358

AN:

151914

Hom.:

5938

Cov.:

show subpopulations

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.:

AF XY:

0.294

AC XY:

71838

AN XY:

244172

show subpopulations

African (AFR)

AF:

0.180

AC:

2332

AN:

12966

American (AMR)

AF:

0.322

AC:

7781

AN:

24178

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

2701

AN:

12462

East Asian (EAS)

AF:

0.339

AC:

9224

AN:

27216

South Asian (SAS)

AF:

0.260

AC:

13310

AN:

51216

European-Finnish (FIN)

AF:

0.378

AC:

13462

AN:

35612

Middle Eastern (MID)

AF:

0.215

AC:

717

AN:

3332

European-Non Finnish (NFE)

AF:

0.298

AC:

79265

AN:

265548

Other (OTH)

AF:

0.286

AC:

6920

AN:

24168

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

4578

9156

13733

18311

22889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

732

1464

2196

2928

3660

<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:

0.272

AC:

41397

AN:

152034

Hom.:

5949

Cov.:

AF XY:

0.275

AC XY:

20390

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.185

AC:

7669

AN:

41508

American (AMR)

AF:

0.283

AC:

4321

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

796

AN:

3470

East Asian (EAS)

AF:

0.365

AC:

1872

AN:

5130

South Asian (SAS)

AF:

0.249

AC:

1202

AN:

4818

European-Finnish (FIN)

AF:

0.389

AC:

4091

AN:

10526

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.302

AC:

20499

AN:

67976

Other (OTH)

AF:

0.278

AC:

588

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

1463

2925

4388

5850

7313

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.292

Hom.:

29220

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

(source)

DANN

Benign

0.62

PhyloP100

1.9

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