rs11421222

Variant names:

• chr9-122629491-CAA-C
• rs11421222
• NM_001004450.3:c.40_41delTT

Your query was ambiguous. Multiple possible variants found:

• chr9-122629491-CAA-C
• chr9-122629491-CAA-CA
• chr9-122629491-CAA-CAAA
• chr9-122629491-CAA-CAAAA
• chr9-122629491-CAA-CAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001004450.3(OR1B1):​c.40_41delTT​(p.Leu14AlafsTer8) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000686 in 1,457,442 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: OR1B1 NM_001004450.3 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.75
• Publications: 0 publications found

Genes affected

OR1B1 (HGNC:8181): (olfactory receptor family 1 subfamily B member 1) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jun 2015]

ENSG00000234156 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004450.3. 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
	OR1B1	NM_001004450.3	MANE Select	c.40_41delTT	p.Leu14AlafsTer8	frameshift	Exon 2 of 2	NP_001004450.2
	OR1B1	NM_001409693.1		c.40_41delTT	p.Leu14AlafsTer8	frameshift	Exon 2 of 2	NP_001396622.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR1B1	ENST00000623530.2	TSL:6 MANE Select	c.40_41delTT	p.Leu14AlafsTer8	frameshift	Exon 2 of 2	ENSP00000485577.2
	OR1B1	ENST00000707075.1		c.40_41delTT	p.Leu14AlafsTer8	frameshift	Exon 2 of 2	ENSP00000516726.1
	ENSG00000234156	ENST00000419604.1	TSL:5	n.279-7609_279-7608delAA		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457442 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 724934

African (AFR) AF: 0.00 AC: 0 AN: 33308

American (AMR) AF: 0.00 AC: 0 AN: 43978

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25916

East Asian (EAS) AF: 0.00 AC: 0 AN: 39668

South Asian (SAS) AF: 0.00 AC: 0 AN: 85486

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53296

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5750

European-Non Finnish (NFE) AF: 9.01e-7 AC: 1 AN: 1109824

Other (OTH) AF: 0.00 AC: 0 AN: 60216

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11421222; hg19: chr9-125391770;