9-133205930-AAC-GAT

Variant names:

• chr9-133205930-AAC-GAT
• NM_014581.4:c.499_501delGTTinsATC
• OBP2B p.Val167Ile

Variant summary

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

The NM_014581.4(OBP2B):​c.499_501delGTTinsATC​(p.Val167Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 35)
• Consequence: OBP2B NM_014581.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 0 publications found

Genes affected

OBP2B (HGNC:23381): (odorant binding protein 2B) Predicted to enable small molecule binding activity. Predicted to be involved in chemosensory behavior. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014581.4. 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
	OBP2B	NM_014581.4	MANE Select	c.499_501delGTTinsATC	p.Val167Ile	missense	N/A	NP_055396.1	Q9NPH6-1
	OBP2B	NM_001288987.2		c.499_501delGTTinsATC	p.Val167Ile	missense	N/A	NP_001275916.1	Q9NPH6-1
	OBP2B	NR_110242.2		n.656_658delGTTinsATC		non_coding_transcript_exon	Exon 7 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OBP2B	ENST00000372034.8	TSL:1 MANE Select	c.499_501delGTTinsATC	p.Val167Ile	missense	N/A	ENSP00000361104.3	Q9NPH6-1
	OBP2B	ENST00000618116.4	TSL:1	c.499_501delGTTinsATC	p.Val167Ile	missense	N/A	ENSP00000484615.1	Q9NPH6-1
	OBP2B	ENST00000461961.2	TSL:1	n.407_409delGTTinsATC		non_coding_transcript_exon	Exon 5 of 6

Frequencies

GnomAD3 genomes Cov.: 35

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-136081317;