rs10925027

Positions:

• chr1-247449260-T-C
• chr1-247449260-T-G

Variant summary

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

The NM_001004492.2(OR2B11):​c.*1769A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,100 control chromosomes in the GnomAD database, including 25,474 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 0.57 (25463 hom., cov: 33)
  • Exomes 𝑓: 0.57 (11 hom.)
• Consequence: OR2B11 NM_001004492.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.*1769A>G		3_prime_UTR_variant	2/2	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.3377A>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.*1769A>G		3_prime_UTR_variant	2/2		NM_001004492.2	ENSP00000492892	P1
OR2B11	ENST00000641527.1	c.*1769A>G		3_prime_UTR_variant	3/3			ENSP00000493421	P1
OR2B11	ENST00000641613.1	n.3377A>G		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87197 AN: 151922 Hom.: 25452 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.567 AC: 34 AN: 60 Hom.: 11 Cov.: 0 AF XY: 0.667 AC XY: 24 AN XY: 36

Gnomad4 EAS exome AF: 0.571

Gnomad4 FIN exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.574 AC: 87243 AN: 152040 Hom.: 25463 Cov.: 33 AF XY: 0.571 AC XY: 42450 AN XY: 74310

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.577

Alfa AF: 0.602 Hom.: 37218

Bravo AF: 0.567

Asia WGS AF: 0.479 AC: 1664 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10925027; hg19: chr1-247612562;