dbSNP rs4489787: OR8S21P:n.21A>G (chr12-48417317-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000609970.1(OR8S21P):n.21A>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 0.101 in 152,204 control chromosomes in the GnomAD database, including 835 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 ( 834 hom., cov: 32)

Exomes 𝑓: 0.25 ( 1 hom. )

Consequence

OR8S21P
ENST00000609970.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.87

Publications

15 publications found

Variant links:

Genes affected

OR8S21P (HGNC:31317): (olfactory receptor family 8 subfamily S member 21 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]

OR8S21P links:

ENSG00000257735 (HGNC:):

ENSG00000257735 links:

C12orf54 (HGNC:28553): (chromosome 12 open reading frame 54)

C12orf54 links:

Genome browser will be placed here

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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
OR8S21P		n.48417317T>C	intragenic_variant
C12orf54	XM_017018796.2 link	c.-523+3735T>C	intron_variant	Intron 1 of 12	XP_016874285.1
C12orf54	XM_011537896.3 link	c.-449+3735T>C	intron_variant	Intron 1 of 10	XP_011536198.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
OR8S21P	ENST00000609970.1 link	n.21A>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000257735	ENST00000548257.1 link	n.238-24770T>C	intron_variant	Intron 3 of 3	4
ENSG00000257735	ENST00000717864.1 link	n.232-24770T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15357

AN:

152054

Hom.:

833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0803

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.0954

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.0325

Gnomad SAS

AF:

0.0665

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.131

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.222

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)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.101

AC:

15356

AN:

152172

Hom.:

834

Cov.:

AF XY:

0.0987

AC XY:

7340

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0803

AC:

3332

AN:

41518

American (AMR)

AF:

0.0952

AC:

1456

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

485

AN:

3472

East Asian (EAS)

AF:

0.0326

AC:

169

AN:

5182

South Asian (SAS)

AF:

0.0659

AC:

318

AN:

4826

European-Finnish (FIN)

AF:

0.106

AC:

1122

AN:

10580

Middle Eastern (MID)

AF:

0.130

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.118

AC:

8053

AN:

67990

Other (OTH)

AF:

0.122

AC:

258

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

696

1391

2087

2782

3478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.112

Hom.:

4353

Bravo

AF:

0.0987

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.079

(source)

DANN

Benign

0.56

PhyloP100

-2.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs4489787

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over