17-20467453-GG-AA

Variant names:

• chr17-20467453-GG-AA
• NM_001367292.2:c.17_18delCCinsTT
• LGALS9B p.Ser6Phe

Variant summary

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

The NM_001367292.2(LGALS9B):​c.17_18delCCinsTT​(p.Ser6Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S6C) has been classified as Benign.

• Frequency: Genomes: not found (cov: 7)
• Consequence: LGALS9B NM_001367292.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 0 publications found

Genes affected

LGALS9B (HGNC:24842): (galectin 9B) This gene was initially thought to represent a pseudogene of galectin 9; however, this transcript has good exon-intron structure and encodes a predicted protein of the same size as and highly similar to galectin 9. This gene is one of two similar loci on chromosome 17p similar to galectin 9 and now thought to be protein-encoding. This gene is the more centromeric gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367292.2. 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
	LGALS9B	NM_001367292.2	MANE Select	c.17_18delCCinsTT	p.Ser6Phe	missense	N/A	NP_001354221.1	Q3B8N2-1
	LGALS9B	NM_001042685.3		c.17_18delCCinsTT	p.Ser6Phe	missense	N/A	NP_001036150.1	Q3B8N2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LGALS9B	ENST00000423676.8	TSL:1 MANE Select	c.17_18delCCinsTT	p.Ser6Phe	missense	N/A	ENSP00000388841.3	Q3B8N2-1
	LGALS9B	ENST00000324290.5	TSL:5	c.17_18delCCinsTT	p.Ser6Phe	missense	N/A	ENSP00000315564.5	Q3B8N2-2
	LGALS9B	ENST00000897463.1		c.17_18delCCinsTT	p.Ser6Phe	missense	N/A	ENSP00000567522.1

Frequencies

GnomAD3 genomes Cov.: 7

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

GnomAD4 genome Cov.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.90

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: chr17-20370766;