Genetic Variant OR2AF1P:n.402A>G (chrX-131619414-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 ENST00000836463.1(ENSG00000286060):n.1327A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 110,158 control chromosomes in the GnomAD database, including 5,557 homozygotes. There are 11,361 hemizygotes in GnomAD. 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 0.36 ( 5555 hom., 11357 hem., cov: 22)

Exomes 𝑓: 0.80 ( 2 hom. 4 hem. )

Consequence

ENSG00000286060
ENST00000836463.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.67

Publications

0 publications found

Variant links:

Genes affected

OR2AF1P (HGNC:14719): (olfactory receptor family 2 subfamily AF member 1 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]

OR2AF1P links:

ENSG00000286060 (HGNC:):

ENSG00000286060 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836463.1. 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
OR2AF1P	ENST00000454899.2	TSL:6	n.402A>G	non_coding_transcript_exon	Exon 1 of 1
ENSG00000286060	ENST00000836463.1		n.1327A>G	non_coding_transcript_exon	Exon 7 of 7
ENSG00000286060	ENST00000836464.1		n.*9A>G	downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

39763

AN:

110092

Hom.:

5560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.573

Gnomad EAS

AF:

0.396

Gnomad SAS

AF:

0.418

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.476

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.354

GnomAD4 exome

AF:

0.800

AC:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

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:

0.800

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.361

AC:

39756

AN:

110148

Hom.:

5555

Cov.:

AF XY:

0.350

AC XY:

11357

AN XY:

32488

show subpopulations

African (AFR)

AF:

0.230

AC:

6991

AN:

30415

American (AMR)

AF:

0.336

AC:

3463

AN:

10319

Ashkenazi Jewish (ASJ)

AF:

0.573

AC:

1498

AN:

2616

East Asian (EAS)

AF:

0.397

AC:

1369

AN:

3447

South Asian (SAS)

AF:

0.419

AC:

1070

AN:

2553

European-Finnish (FIN)

AF:

0.380

AC:

2190

AN:

5756

Middle Eastern (MID)

AF:

0.467

AC:

AN:

212

European-Non Finnish (NFE)

AF:

0.422

AC:

22206

AN:

52649

Other (OTH)

AF:

0.350

AC:

525

AN:

1502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

900

1800

2701

3601

4501

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

392

784

1176

1568

1960

<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:

0.404

Hom.:

50002

Bravo

AF:

0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.012

(source)

DANN

Benign

0.47

PhyloP100

-1.7

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