Genetic Variant ENST00000514684.1:n.933G>A (chr1-159279069-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 ENST00000514684.1(OR10J2P):n.933G>A 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 0.09 in 168,166 control chromosomes in the GnomAD database, including 1,367 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 0.090 ( 1220 hom., cov: 32)

Exomes 𝑓: 0.090 ( 147 hom. )

Consequence

OR10J2P
ENST00000514684.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105

Publications

6 publications found

Variant links:

Genes affected

OR10J2P (HGNC:14991): (olfactory receptor family 10 subfamily J member 2 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]

OR10J2P 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=-0.43).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10J2P		n.159279069C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR10J2P	ENST00000514684.1 link	n.933G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.0900

AC:

13678

AN:

152002

Hom.:

1220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0846

Gnomad AMI

AF:

0.0440

Gnomad AMR

AF:

0.0997

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.0702

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0504

Gnomad OTH

AF:

0.0861

GnomAD4 exome

AF:

0.0898

AC:

1441

AN:

16046

Hom.:

147

Cov.:

AF XY:

0.0909

AC XY:

847

AN XY:

9314

show subpopulations

African (AFR)

AF:

0.0534

AC:

AN:

412

American (AMR)

AF:

0.110

AC:

102

AN:

924

Ashkenazi Jewish (ASJ)

AF:

0.0735

AC:

AN:

204

East Asian (EAS)

AF:

0.477

AC:

416

AN:

872

South Asian (SAS)

AF:

0.206

AC:

237

AN:

1150

European-Finnish (FIN)

AF:

0.0663

AC:

132

AN:

1992

Middle Eastern (MID)

AF:

0.0701

AC:

AN:

970

European-Non Finnish (NFE)

AF:

0.0452

AC:

389

AN:

8606

Other (OTH)

AF:

0.0655

AC:

AN:

916

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

108

161

215

269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

<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:

0.0900

AC:

13689

AN:

152120

Hom.:

1220

Cov.:

AF XY:

0.0949

AC XY:

7060

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0845

AC:

3508

AN:

41500

American (AMR)

AF:

0.0999

AC:

1526

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

394

AN:

3466

East Asian (EAS)

AF:

0.535

AC:

2764

AN:

5166

South Asian (SAS)

AF:

0.224

AC:

1079

AN:

4816

European-Finnish (FIN)

AF:

0.0702

AC:

744

AN:

10592

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0504

AC:

3428

AN:

67994

Other (OTH)

AF:

0.0862

AC:

182

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

580

1160

1739

2319

2899

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

162

324

486

648

810

<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:

0.0672

Hom.:

502

Bravo

AF:

0.0927

Asia WGS

AF:

0.316

AC:

1098

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.10

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