1-247453734-G-T

Position:

• chr1-247453734-G-T

Variant summary

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

The NM_001004492.2(OR2B11):​c.-1752C>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 0.704 in 152,108 control chromosomes in the GnomAD database, including 37,764 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 0.70 (37761 hom., cov: 32)
  • Exomes 𝑓: 0.70 (3 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

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 (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.-1752C>A		5_prime_UTR_variant	2/2	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.482+1219C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-1752C>A		5_prime_UTR_variant	2/2		NM_001004492.2	ENSP00000492892.1
OR2B11	ENST00000641527.1	c.-1101-651C>A		intron_variant				ENSP00000493421.1
OR2B11	ENST00000641613.1	n.482+1219C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106957 AN: 151980 Hom.: 37721 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.668

GnomAD4 exome AF: 0.700 AC: 7 AN: 10 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.704 AC: 107053 AN: 152098 Hom.: 37761 Cov.: 32 AF XY: 0.701 AC XY: 52074 AN XY: 74322

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.667

Alfa AF: 0.686 Hom.: 50988

Bravo AF: 0.709

Asia WGS AF: 0.622 AC: 2164 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	2.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4353135; hg19: chr1-247617036;