rs55646866

Variant names:

• chr1-247457083-C-T
• rs55646866
• NM_001004492.2:c.-3083+556G>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.-3083+556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,156 control chromosomes in the GnomAD database, including 784 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 0.090 (784 hom., cov: 31)
• Consequence: OR2B11 NM_001004492.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 8 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=-0.94).
• 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.-3083+556G>A		intron_variant	Intron 1 of 1	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.370+556G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-3083+556G>A		intron_variant	Intron 1 of 1		NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1	c.-1214+556G>A		intron_variant	Intron 1 of 2			ENSP00000493421.1
OR2B11	ENST00000641613.1	n.370+556G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13772 AN: 152038 Hom.: 786 Cov.: 31

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0644

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0952

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

GnomAD4 genome AF: 0.0905 AC: 13765 AN: 152156 Hom.: 784 Cov.: 31 AF XY: 0.0926 AC XY: 6884 AN XY: 74366

African (AFR) AF: 0.0219 AC: 911 AN: 41520

American (AMR) AF: 0.0889 AC: 1360 AN: 15300

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

East Asian (EAS) AF: 0.0645 AC: 334 AN: 5176

South Asian (SAS) AF: 0.0608 AC: 293 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1829 AN: 10572

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8116 AN: 67980

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.103 Hom.: 117

Bravo AF: 0.0823

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.47
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs55646866; hg19: chr1-247620385;