dbSNP rs72655376: OR2B11:c.-3083+102G>A (chr1-247457537-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 NM_001004492.2(OR2B11):c.-3083+102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,438 control chromosomes in the GnomAD database, including 853 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 0.10 ( 853 hom., cov: 32)

Exomes 𝑓: 0.096 ( 0 hom. )

Consequence

OR2B11
NM_001004492.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.654

Publications

0 publications found

Variant links:

Genes affected

OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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]

OR2B11 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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B11	NM_001004492.2 link	c.-3083+102G>A		intron_variant	Intron 1 of 1	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1 link	n.370+102G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
OR2B11	ENST00000641149.2 link	c.-3083+102G>A	intron_variant	Intron 1 of 1	NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1 link	c.-1214+102G>A	intron_variant	Intron 1 of 2		ENSP00000493421.1
OR2B11	ENST00000641613.1 link	n.370+102G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15507

AN:

152040

Hom.:

855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0618

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.0926

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.0650

Gnomad SAS

AF:

0.0602

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.101

GnomAD4 exome

AF:

0.0964

AC:

AN:

280

Hom.:

AF XY:

0.0904

AC XY:

AN XY:

188

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.105

AC:

AN:

Middle Eastern (MID)

AF:

0.250

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0979

AC:

AN:

194

Other (OTH)

AF:

0.0556

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

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:

0.102

AC:

15509

AN:

152158

Hom.:

853

Cov.:

AF XY:

0.104

AC XY:

7741

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0618

AC:

2566

AN:

41524

American (AMR)

AF:

0.0925

AC:

1414

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

542

AN:

3470

East Asian (EAS)

AF:

0.0652

AC:

336

AN:

5154

South Asian (SAS)

AF:

0.0605

AC:

292

AN:

4826

European-Finnish (FIN)

AF:

0.173

AC:

1826

AN:

10568

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8142

AN:

68008

Other (OTH)

AF:

0.100

AC:

212

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

724

1449

2173

2898

3622

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<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:

0.0801

Hom.:

151

Bravo

AF:

0.0954

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

(source)

DANN

Benign

0.49

PhyloP100

-0.65

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