dbSNP rs6672995: OR2B11:c.-3175C>T (chr1-247457731-G-A) – 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.-3175C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,180 control chromosomes in the GnomAD database, including 1,956 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 0.15 ( 1956 hom., cov: 32)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

OR2B11
NM_001004492.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.36

Publications

28 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=-0.79).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B11	NM_001004492.2 link	c.-3175C>T		5_prime_UTR_variant	Exon 1 of 2	ENST00000641149.2	NP_001004492.1	Q5JQS5A0A126GVY5
OR2B11	NR_169840.1 link	n.278C>T		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
OR2B11	ENST00000641149.2 link	c.-3175C>T	5_prime_UTR_variant	Exon 1 of 2	NM_001004492.2	ENSP00000492892.1	Q5JQS5
OR2B11	ENST00000641613.1 link	n.278C>T	non_coding_transcript_exon_variant	Exon 1 of 5
OR2B11	ENST00000641527.1 link	c.-1306C>T	5_prime_UTR_variant	Exon 1 of 3		ENSP00000493421.1	Q5JQS5

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22726

AN:

152032

Hom.:

1957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0761

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.0671

Gnomad SAS

AF:

0.0925

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.144

GnomAD4 exome

AF:

0.133

AC:

AN:

Hom.:

Cov.:

AF XY:

0.136

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.100

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.100

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.149

AC:

22731

AN:

152150

Hom.:

1956

Cov.:

AF XY:

0.151

AC XY:

11260

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.0760

AC:

3157

AN:

41516

American (AMR)

AF:

0.186

AC:

2840

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

744

AN:

3472

East Asian (EAS)

AF:

0.0673

AC:

348

AN:

5172

South Asian (SAS)

AF:

0.0932

AC:

449

AN:

4818

European-Finnish (FIN)

AF:

0.237

AC:

2502

AN:

10570

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.178

AC:

12115

AN:

67996

Other (OTH)

AF:

0.143

AC:

302

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

984

1969

2953

3938

4922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

242

484

726

968

1210

<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:

0.168

Hom.:

3245

Bravo

AF:

0.141

Asia WGS

AF:

0.0940

AC:

326

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

5.4

(source)

DANN

Benign

0.34

PhyloP100

2.4

PromoterAI

-0.0012

Neutral

(source)

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