6-8413588-CA-GG

Variant names:

• chr6-8413588-CA-GG
• NM_001370479.2:c.1070_1071delTGinsCC
• SLC35B3 p.Val357Ala

Variant summary

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

The NM_001370479.2(SLC35B3):​c.1070_1071delTGinsCC​(p.Val357Ala) 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC35B3 NM_001370479.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507
• Publications: 0 publications found

Genes affected

SLC35B3 (HGNC:21601): (solute carrier family 35 member B3) This gene is a member of the solute carrier family. The encoded protein is involved in the transport of 3-prime phosphoadenosine 5-prime phosphosulfate (PAPS) from the nucleus or the cytosol to the Golgi lumen. This gene has been reported to be expressed preferentially in the human colon tissues. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

ENSG00000285216 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370479.2. 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
	SLC35B3	NM_001370479.2	MANE Select	c.1070_1071delTGinsCC	p.Val357Ala	missense	N/A	NP_001357408.1	A0A024QZW4
	SLC35B3	NM_001142540.2		c.1166_1167delTGinsCC	p.Val389Ala	missense	N/A	NP_001136012.1	Q9H1N7-1
	SLC35B3	NM_001142541.3		c.1166_1167delTGinsCC	p.Val389Ala	missense	N/A	NP_001136013.1	Q9H1N7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35B3	ENST00000710437.1	MANE Select	c.1070_1071delTGinsCC	p.Val357Ala	missense	N/A	ENSP00000518269.1	A0A024QZW4
	SLC35B3	ENST00000379660.4	TSL:1	c.1166_1167delTGinsCC	p.Val389Ala	missense	N/A	ENSP00000368981.4	Q9H1N7-1
	SLC35B3	ENST00000644923.2		c.1166_1167delTGinsCC	p.Val389Ala	missense	N/A	ENSP00000496368.1	Q9H1N7-1

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		0.51

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: chr6-8413821;