NM_001532.3:c.556delG

Variant names:

• chr11-66367863-AC-A
• rs8187649
• NM_001532.3:c.556delG

Variant summary

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

The NM_001532.3(SLC29A2):​c.556delG​(p.Val186TrpfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC29A2 NM_001532.3 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 2 publications found

Genes affected

SLC29A2 (HGNC:11004): (solute carrier family 29 member 2) The uptake of nucleosides by transporters, such as SLC29A2, is essential for nucleotide synthesis by salvage pathways in cells that lack de novo biosynthetic pathways. Nucleoside transport also plays a key role in the regulation of many physiologic processes through its effect on adenosine concentration at the cell surface (Griffiths et al., 1997 [PubMed 9396714]).[supplied by OMIM, Nov 2008]

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_001532.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A2	NM_001532.3	MANE Select	c.556delG	p.Val186TrpfsTer26	frameshift	Exon 6 of 12	NP_001523.2
	SLC29A2	NM_001300868.2		c.556delG	p.Val186TrpfsTer26	frameshift	Exon 8 of 14	NP_001287797.1
	SLC29A2	NM_001300869.2		c.556delG	p.Val186TrpfsTer26	frameshift	Exon 8 of 13	NP_001287798.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC29A2	ENST00000357440.7	TSL:1 MANE Select	c.556delG	p.Val186TrpfsTer26	frameshift	Exon 6 of 12	ENSP00000350024.2
	SLC29A2	ENST00000311161.11	TSL:1	c.556delG	p.Val186TrpfsTer26	frameshift	Exon 7 of 12	ENSP00000311250.7
	SLC29A2	ENST00000540386.5	TSL:1	n.556delG		non_coding_transcript_exon	Exon 6 of 12	ENSP00000444870.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.051

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs8187649; hg19: chr11-66135334;