chr15-84933212-T-TG

Variant names:

• chr15-84933212-T-TG
• rs17215989
• NM_004213.5:c.1153dupG

Variant summary

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

The NM_004213.5(SLC28A1):​c.1153dupG​(p.Val385GlyfsTer11) 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: 32)
• Consequence: SLC28A1 NM_004213.5 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 3 publications found

Genes affected

SLC28A1 (HGNC:11001): (solute carrier family 28 member 1) Enables azole transmembrane transporter activity; cytidine transmembrane transporter activity; and uridine transmembrane transporter activity. Involved in azole transmembrane transport; nucleoside transport; and pyrimidine-containing compound transmembrane transport. Located in cytosol; nuclear speck; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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_004213.5. 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
	SLC28A1	NM_004213.5	MANE Select	c.1153dupG	p.Val385GlyfsTer11	frameshift	Exon 13 of 19	NP_004204.3
	SLC28A1	NM_001287762.2		c.1153dupG	p.Val385GlyfsTer11	frameshift	Exon 12 of 18	NP_001274691.1
	SLC28A1	NM_001321722.2		c.1153dupG	p.Val385GlyfsTer11	frameshift	Exon 13 of 19	NP_001308651.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.1153dupG	p.Val385GlyfsTer11	frameshift	Exon 13 of 19	ENSP00000378074.1
	SLC28A1	ENST00000286749.3	TSL:1	c.1153dupG	p.Val385GlyfsTer11	frameshift	Exon 12 of 18	ENSP00000286749.3
	SLC28A1	ENST00000538177.5	TSL:2	c.1083+9104dupG		intron	N/A	ENSP00000443752.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.22

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs17215989; hg19: chr15-85476443;