rs66711223

Variant names:

• chr1-247454527-C-T
• rs66711223
• NM_001004492.2:c.-2545G>A

Variant summary

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

The NM_001004492.2(OR2B11):​c.-2545G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 152,436 control chromosomes in the GnomAD database, including 578 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 0.079 (577 hom., cov: 32)
  • Exomes 𝑓: 0.067 (1 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.-2545G>A		5_prime_UTR_variant	Exon 2 of 2	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.482+426G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-2545G>A		5_prime_UTR_variant	Exon 2 of 2		NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1	c.-1102+426G>A		intron_variant	Intron 2 of 2			ENSP00000493421.1
OR2B11	ENST00000641613.1	n.482+426G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11971 AN: 152110 Hom.: 576 Cov.: 32

Gnomad AFR AF: 0.0471

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0449

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0884

GnomAD4 exome AF: 0.0673 AC: 14 AN: 208 Hom.: 1 Cov.: 0 AF XY: 0.0873 AC XY: 11 AN XY: 126

Gnomad4 AFR exome AF: 0.0833

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0385

Gnomad4 NFE exome AF: 0.0784

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.0787 AC: 11973 AN: 152228 Hom.: 577 Cov.: 32 AF XY: 0.0778 AC XY: 5787 AN XY: 74430

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0453

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0873 Hom.: 72

Bravo AF: 0.0779

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs66711223; hg19: chr1-247617829;