NM_001004492.2:c.-3082-976G>A

Variant names:

• chr1-247456040-C-T
• rs72655372
• NM_001004492.2:c.-3082-976G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004492.2(OR2B11):​c.-3082-976G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 152,212 control chromosomes in the GnomAD database, including 798 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 0.093 (798 hom., cov: 32)
• Consequence: OR2B11 NM_001004492.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 0 publications found

Genes affected

OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004492.2. 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
	OR2B11	NM_001004492.2	MANE Select	c.-3082-976G>A		intron	N/A	NP_001004492.1	Q5JQS5
	OR2B11	NR_169840.1		n.371-976G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B11	ENST00000641149.2	MANE Select	c.-3082-976G>A		intron	N/A	ENSP00000492892.1	Q5JQS5
	OR2B11	ENST00000641527.1		c.-1213-976G>A		intron	N/A	ENSP00000493421.1	Q5JQS5
	OR2B11	ENST00000641613.1		n.371-976G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14171 AN: 152094 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0955

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0931 AC: 14171 AN: 152212 Hom.: 798 Cov.: 32 AF XY: 0.0953 AC XY: 7092 AN XY: 74402

African (AFR) AF: 0.0313 AC: 1298 AN: 41536

American (AMR) AF: 0.0893 AC: 1366 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3472

East Asian (EAS) AF: 0.0648 AC: 336 AN: 5186

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4824

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8134 AN: 68006

Other (OTH) AF: 0.0950 AC: 200 AN: 2106

Alfa AF: 0.105 Hom.: 117

Bravo AF: 0.0853

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.35
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs72655372; hg19: chr1-247619342;