dbSNP rs6971999: OR2F1:c.-177A>G (chr7-143958955-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_012369.3(OR2F1):c.-177A>G variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,196 control chromosomes in the GnomAD database, including 2,704 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 0.16 ( 2704 hom., cov: 30)

Exomes 𝑓: 0.063 ( 0 hom. )

Consequence

OR2F1
NM_012369.3 splice_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

Publications

3 publications found

Variant links:

Genes affected

OR2F1 (HGNC:8246): (olfactory receptor family 2 subfamily F member 1) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

OR2F1 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012369.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2F1	NM_012369.3	MANE Select	c.-177A>G		splice_region	Exon 2 of 3	NP_036501.2
	OR2F1	NM_012369.3	MANE Select	c.-177A>G		5_prime_UTR	Exon 2 of 3	NP_036501.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OR2F1	ENST00000641412.1	MANE Select	c.-177A>G	splice_region	Exon 2 of 3	ENSP00000493004.1
OR2F1	ENST00000641412.1	MANE Select	c.-177A>G	5_prime_UTR	Exon 2 of 3	ENSP00000493004.1
OR2F1	ENST00000641986.1		n.96A>G	splice_region non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24691

AN:

151074

Hom.:

2694

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.129

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.0990

Gnomad EAS

AF:

0.177

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0868

Gnomad OTH

AF:

0.163

GnomAD4 exome

AF:

0.0625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0833

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

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

GnomAD4 genome

AF:

0.164

AC:

24758

AN:

151180

Hom.:

2704

Cov.:

AF XY:

0.165

AC XY:

12196

AN XY:

73824

show subpopulations

African (AFR)

AF:

0.285

AC:

11707

AN:

41036

American (AMR)

AF:

0.219

AC:

3328

AN:

15198

Ashkenazi Jewish (ASJ)

AF:

0.0990

AC:

343

AN:

3464

East Asian (EAS)

AF:

0.177

AC:

906

AN:

5126

South Asian (SAS)

AF:

0.123

AC:

586

AN:

4768

European-Finnish (FIN)

AF:

0.143

AC:

1485

AN:

10366

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0868

AC:

5893

AN:

67922

Other (OTH)

AF:

0.168

AC:

351

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

921

1841

2762

3682

4603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.113

Hom.:

710

Bravo

AF:

0.181

Asia WGS

AF:

0.172

AC:

598

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

(source)

DANN

Benign

0.79

PhyloP100

0.26

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over