rs72655375

Variant names:

• chr1-247456211-C-T
• rs72655375
• NM_001004492.2:c.-3082-1147G>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.-3082-1147G>A 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 152,160 control chromosomes in the GnomAD database, including 792 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 (792 hom., cov: 32)
• Consequence: OR2B11 NM_001004492.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• 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=-0.95).
• 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.-3082-1147G>A		intron_variant	Intron 1 of 1	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.371-1147G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-3082-1147G>A		intron_variant	Intron 1 of 1		NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1	c.-1213-1147G>A		intron_variant	Intron 1 of 2			ENSP00000493421.1
OR2B11	ENST00000641613.1	n.371-1147G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14156 AN: 152042 Hom.: 794 Cov.: 32

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0645

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0940

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

GnomAD4 genome AF: 0.0930 AC: 14156 AN: 152160 Hom.: 792 Cov.: 32 AF XY: 0.0953 AC XY: 7086 AN XY: 74390

African (AFR) AF: 0.0313 AC: 1301 AN: 41520

American (AMR) AF: 0.0892 AC: 1363 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.0647 AC: 335 AN: 5180

South Asian (SAS) AF: 0.0604 AC: 291 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10584

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

European-Non Finnish (NFE) AF: 0.119 AC: 8122 AN: 67996

Other (OTH) AF: 0.0935 AC: 197 AN: 2108

Alfa AF: 0.105 Hom.: 115

Bravo AF: 0.0852

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs72655375; hg19: chr1-247619513;