rs6672995

Positions:

• chr1-247457731-G-A

Variant summary

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

The NM_001004492.2(OR2B11):​c.-3175C>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 0.149 in 152,180 control chromosomes in the GnomAD database, including 1,956 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 0.15 (1956 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.36

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2B11	NM_001004492.2	c.-3175C>T		5_prime_UTR_variant	1/2	ENST00000641149.2
OR2B11	NR_169840.1	n.278C>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2B11	ENST00000641149.2	c.-3175C>T		5_prime_UTR_variant	1/2		NM_001004492.2	P1
OR2B11	ENST00000641527.1	c.-1306C>T		5_prime_UTR_variant	1/3			P1
OR2B11	ENST00000641613.1	n.278C>T		non_coding_transcript_exon_variant	1/5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22726 AN: 152032 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.144

GnomAD4 exome AF: 0.133 AC: 4 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.149 AC: 22731 AN: 152150 Hom.: 1956 Cov.: 32 AF XY: 0.151 AC XY: 11260 AN XY: 74362

Gnomad4 AFR AF: 0.0760

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.0673

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.143

Alfa AF: 0.163 Hom.: 768

Bravo AF: 0.141

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6672995; hg19: chr1-247621033;