chr1-247454207-G-A

Position:

• chr1-247454207-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.-2225C>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 0.0796 in 151,356 control chromosomes in the GnomAD database, including 585 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 (574 hom., cov: 33)
  • Exomes 𝑓: 0.13 (11 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.957

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2B11	NM_001004492.2	c.-2225C>T		5_prime_UTR_variant	2/2	ENST00000641149.2
OR2B11	NR_169840.1	n.482+746C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2B11	ENST00000641149.2	c.-2225C>T		5_prime_UTR_variant	2/2		NM_001004492.2	P1
OR2B11	ENST00000641527.1	c.-1102+746C>T		intron_variant				P1
OR2B11	ENST00000641613.1	n.482+746C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 11973 AN: 150658 Hom.: 573 Cov.: 33

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.00214

Gnomad SAS AF: 0.0452

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.147

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0889

GnomAD4 exome AF: 0.128 AC: 75 AN: 584 Hom.: 11 Cov.: 0 AF XY: 0.126 AC XY: 53 AN XY: 422

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0167

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.0794 AC: 11975 AN: 150772 Hom.: 574 Cov.: 33 AF XY: 0.0786 AC XY: 5792 AN XY: 73684

Gnomad4 AFR AF: 0.0480

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.00214

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.0929

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0870 Hom.: 69

Bravo AF: 0.0780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs67745645; hg19: chr1-247617509;