NM_001004492.2:c.-3082-895A>G

Variant names:

• chr1-247455959-T-C
• rs72655371
• NM_001004492.2:c.-3082-895A>G

Variant summary

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

The NM_001004492.2(OR2B11):​c.-3082-895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.093 in 152,260 control chromosomes in the GnomAD database, including 793 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 (793 hom., cov: 33)
• Consequence: OR2B11 NM_001004492.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.-3082-895A>G		intron_variant	Intron 1 of 1	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.371-895A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-3082-895A>G		intron_variant	Intron 1 of 1		NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1	c.-1213-895A>G		intron_variant	Intron 1 of 2			ENSP00000493421.1
OR2B11	ENST00000641613.1	n.371-895A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14167 AN: 152142 Hom.: 795 Cov.: 33

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.0930 AC: 14167 AN: 152260 Hom.: 793 Cov.: 33 AF XY: 0.0953 AC XY: 7093 AN XY: 74444

African (AFR) AF: 0.0313 AC: 1302 AN: 41572

American (AMR) AF: 0.0892 AC: 1364 AN: 15294

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

East Asian (EAS) AF: 0.0646 AC: 334 AN: 5174

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4826

European-Finnish (FIN) AF: 0.172 AC: 1828 AN: 10598

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

European-Non Finnish (NFE) AF: 0.120 AC: 8129 AN: 68004

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0582 Hom.: 82

Bravo AF: 0.0853

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.57
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs72655371; hg19: chr1-247619261;