rs4266924

Positions:

• chr1-247453832-G-A
• chr1-247453832-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004492.2(OR2B11):​c.-1850C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,166 control chromosomes in the GnomAD database, including 57,130 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 0.87 (57129 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2B11	NM_001004492.2	c.-1850C>T		5_prime_UTR_variant	2/2	ENST00000641149.2
OR2B11	NR_169840.1	n.482+1121C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2B11	ENST00000641149.2	c.-1850C>T		5_prime_UTR_variant	2/2		NM_001004492.2	P1
OR2B11	ENST00000641527.1	c.-1101-749C>T		intron_variant				P1
OR2B11	ENST00000641613.1	n.482+1121C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131715 AN: 152046 Hom.: 57091 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.866 AC: 131808 AN: 152164 Hom.: 57129 Cov.: 32 AF XY: 0.864 AC XY: 64277 AN XY: 74368

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.939

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.869

Alfa AF: 0.866 Hom.: 7703

Bravo AF: 0.868

Asia WGS AF: 0.930 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4266924; hg19: chr1-247617134;