6-25916754-CCA-GCT

Variant names:

• chr6-25916754-CCA-GCT
• NM_001286123.3:c.859_861delTGGinsAGC
• SLC17A2 p.Trp287Ser

Variant summary

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

The NM_001286123.3(SLC17A2):​c.859_861delTGGinsAGC​(p.Trp287Ser) variant causes a missense change. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W287L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC17A2 NM_001286123.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.70
• Publications: 0 publications found

Genes affected

SLC17A2 (HGNC:10930): (solute carrier family 17 member 2) Predicted to enable sialic acid transmembrane transporter activity. Predicted to be involved in sialic acid transport. Predicted to be located in membrane. Predicted to be active in lysosome. Predicted to be integral component of plasma membrane. [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_001286123.3. 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
	SLC17A2	NM_001286123.3	MANE Select	c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	NP_001273052.1	O00624-3
	SLC17A2	NM_005835.4		c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	NP_005826.1	O00624-2
	SLC17A2	NM_001286125.2		c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	NP_001273054.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC17A2	ENST00000377850.8	TSL:5 MANE Select	c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	ENSP00000367081.3	O00624-3
	SLC17A2	ENST00000360488.7	TSL:1	c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	ENSP00000353677.3	O00624-2
	SLC17A2	ENST00000882944.1		c.859_861delTGGinsAGC	p.Trp287Ser	missense	N/A	ENSP00000553003.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.7

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: chr6-25916982;