Genetic Variant OR2B7P:n.386C>T (chr6-28046819-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 ENST00000429302.1(OR2B7P):n.386C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.239 in 163,212 control chromosomes in the GnomAD database, including 5,298 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 0.25 ( 5264 hom., cov: 31)

Exomes 𝑓: 0.072 ( 34 hom. )

Consequence

OR2B7P
ENST00000429302.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.96

Publications

18 publications found

Variant links:

Genes affected

OR2B7P (HGNC:13967): (olfactory receptor family 2 subfamily B member 7 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]

OR2B7P links:

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ZSCAN16-AS1 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=-0.31).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429302.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
OR2B7P	ENST00000429302.1	TSL:6	n.386C>T	non_coding_transcript_exon	Exon 1 of 1
ZSCAN16-AS1	ENST00000660873.1		n.188+13559G>A	intron	N/A
ZSCAN16-AS1	ENST00000716089.1		n.223+13559G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.251

AC:

38104

AN:

151848

Hom.:

5254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.359

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.186

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.241

GnomAD4 exome

AF:

0.0722

AC:

812

AN:

11246

Hom.:

Cov.:

AF XY:

0.0767

AC XY:

408

AN XY:

5320

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

0.0952

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.0556

AC:

AN:

South Asian (SAS)

AF:

0.0455

AC:

AN:

European-Finnish (FIN)

AF:

0.0700

AC:

720

AN:

10280

Middle Eastern (MID)

AF:

0.0505

AC:

AN:

198

European-Non Finnish (NFE)

AF:

0.114

AC:

AN:

510

Other (OTH)

AF:

0.0942

AC:

AN:

138

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.367

Heterozygous variant carriers

124

165

206

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:

0.251

AC:

38147

AN:

151966

Hom.:

5264

Cov.:

AF XY:

0.244

AC XY:

18093

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.359

AC:

14849

AN:

41396

American (AMR)

AF:

0.259

AC:

3947

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

648

AN:

3472

East Asian (EAS)

AF:

0.186

AC:

960

AN:

5164

South Asian (SAS)

AF:

0.161

AC:

775

AN:

4814

European-Finnish (FIN)

AF:

0.141

AC:

1490

AN:

10580

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14665

AN:

67956

Other (OTH)

AF:

0.239

AC:

504

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1393

2786

4178

5571

6964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

390

780

1170

1560

1950

<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:

0.225

Hom.:

7404

Bravo

AF:

0.267

Asia WGS

AF:

0.165

AC:

574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

4.7

(source)

DANN

Benign

0.85

PhyloP100

7.0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over