1-247453734-G-T

Variant names:

• chr1-247453734-G-T
• rs4353135
• NM_001004492.2:c.-1752C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 40 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004492.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B11	NM_001004492.2	MANE Select	c.-1752C>A		5_prime_UTR	Exon 2 of 2	NP_001004492.1
	OR2B11	NR_169840.1		n.482+1219C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B11	ENST00000641149.2	MANE Select	c.-1752C>A		5_prime_UTR	Exon 2 of 2	ENSP00000492892.1
	OR2B11	ENST00000641527.1		c.-1101-651C>A		intron	N/A	ENSP00000493421.1
	OR2B11	ENST00000641613.1		n.482+1219C>A		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 6 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.776 AC: 32228 AN: 41512

American (AMR) AF: 0.697 AC: 10655 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3034 AN: 5164

South Asian (SAS) AF: 0.681 AC: 3290 AN: 4828

European-Finnish (FIN) AF: 0.659 AC: 6940 AN: 10538

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46586 AN: 67986

Other (OTH) AF: 0.667 AC: 1409 AN: 2112

Alfa AF: 0.695 Hom.: 80100

Bravo AF: 0.709

Asia WGS AF: 0.622 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4353135; hg19: chr1-247617036;