rs55646866

Positions:

• chr1-247457083-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.-3083+556G>A		intron_variant		ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.370+556G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-3083+556G>A		intron_variant			NM_001004492.2	ENSP00000492892	P1
OR2B11	ENST00000641527.1	c.-1214+556G>A		intron_variant				ENSP00000493421	P1
OR2B11	ENST00000641613.1	n.370+556G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0219

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0947

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55646866; hg19: chr1-247620385;