rs67745645

Variant names:

• chr1-247454207-G-A
• rs67745645
• NM_001004492.2:c.-2225C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.116 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B11	NM_001004492.2	MANE Select	c.-2225C>T		5_prime_UTR	Exon 2 of 2	NP_001004492.1	Q5JQS5
	OR2B11	NR_169840.1		n.482+746C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B11	ENST00000641149.2	MANE Select	c.-2225C>T		5_prime_UTR	Exon 2 of 2	ENSP00000492892.1	Q5JQS5
	OR2B11	ENST00000641527.1		c.-1102+746C>T		intron	N/A	ENSP00000493421.1	Q5JQS5
	OR2B11	ENST00000641613.1		n.482+746C>T		intron	N/A

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

African (AFR) AF: 0.125 AC: 1 AN: 8

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 10

European-Finnish (FIN) AF: 0.0167 AC: 1 AN: 60

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.150 AC: 70 AN: 468

Other (OTH) AF: 0.0833 AC: 2 AN: 24

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

African (AFR) AF: 0.0480 AC: 1950 AN: 40650

American (AMR) AF: 0.120 AC: 1830 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3466

East Asian (EAS) AF: 0.00214 AC: 11 AN: 5140

South Asian (SAS) AF: 0.0456 AC: 218 AN: 4778

European-Finnish (FIN) AF: 0.0938 AC: 983 AN: 10484

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.0929 AC: 6294 AN: 67740

Other (OTH) AF: 0.0880 AC: 184 AN: 2092

Alfa AF: 0.0870 Hom.: 69

Bravo AF: 0.0780

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.87
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs67745645; hg19: chr1-247617509;