Genetic Variant ENSG00000239920:n.*739+38475A>C (chr11-5552350-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

3 publications found

Variant links:

Genes affected

ENSG00000239920 (HGNC:):

ENSG00000239920 links:

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]

OR52H2P 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=-0.82).

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 link	n.*739+38475A>C		intron_variant	Intron 5 of 7	5		ENSP00000369609.3		A0A2U3TZJ3
OR52H2P	ENST00000514607.1 link	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.:

show subpopulations

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.:

Cov.:

AF XY:

0.253

AC XY:

276

AN XY:

1090

show subpopulations

African (AFR)

AF:

0.231

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.111

AC:

AN:

European-Finnish (FIN)

AF:

0.212

AC:

255

AN:

1200

Middle Eastern (MID)

AF:

0.245

AC:

102

AN:

416

European-Non Finnish (NFE)

AF:

0.219

AC:

AN:

196

Other (OTH)

AF:

0.303

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.237

AC:

35962

AN:

151988

Hom.:

4472

Cov.:

AF XY:

0.232

AC XY:

17235

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.193

AC:

7977

AN:

41434

American (AMR)

AF:

0.275

AC:

4196

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

1156

AN:

3472

East Asian (EAS)

AF:

0.0795

AC:

410

AN:

5154

South Asian (SAS)

AF:

0.116

AC:

560

AN:

4822

European-Finnish (FIN)

AF:

0.205

AC:

2170

AN:

10572

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.275

AC:

18675

AN:

67948

Other (OTH)

AF:

0.244

AC:

513

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1393

2786

4180

5573

6966

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.236

Hom.:

3242

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

(source)

DANN

Benign

0.65

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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