rs948725

chr11-124540039-G-Achr11-124540039-G-Cchr11-124540039-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641958.1(OR8B12):n.876C>T 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 0.807 in 152,208 control chromosomes in the GnomAD database, including 50,091 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 0.81 (50084 hom., cov: 32)
  • Exomes 𝑓: 0.77 (7 hom.)
• Consequence: OR8B12 ENST00000641958.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

Genes affected

OR8B12 (HGNC:15307): (olfactory receptor family 8 subfamily B member 12) 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR8B12	ENST00000641958.1	n.876C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122718 AN: 152068 Hom.: 50034 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.818

GnomAD4 exome AF: 0.773 AC: 17 AN: 22 Hom.: 7 Cov.: 0 AF XY: 0.722 AC XY: 13 AN XY: 18

Gnomad4 NFE exome AF: 0.773

GnomAD4 genome AF: 0.807 AC: 122825 AN: 152186 Hom.: 50084 Cov.: 32 AF XY: 0.810 AC XY: 60229 AN XY: 74396

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.819

Alfa AF: 0.761 Hom.: 55651

Bravo AF: 0.815

Asia WGS AF: 0.852 AC: 2966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.33
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948725; hg19: chr11-124409935;