ENST00000641958.1:n.876C>T

Variant names:

• chr11-124540039-G-A
• rs948725
• ENST00000641958.1:n.876C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR8B12	ENST00000641958.1	n.876C>T		non_coding_transcript_exon_variant	Exon 3 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.773 AC: 17 AN: 22

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.917 AC: 38092 AN: 41548

American (AMR) AF: 0.809 AC: 12368 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2642 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4641 AN: 5164

South Asian (SAS) AF: 0.772 AC: 3717 AN: 4816

European-Finnish (FIN) AF: 0.766 AC: 8119 AN: 10594

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50803 AN: 68002

Other (OTH) AF: 0.819 AC: 1724 AN: 2104

Alfa AF: 0.767 Hom.: 72576

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs948725; hg19: chr11-124409935;