NM_004213.5:c.419_420insGT

Variant names:

• chr15-84895080-C-CTG
• rs17215836
• NM_004213.5:c.419_420insGT

Variant summary

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

The NM_004213.5(SLC28A1):​c.419_420insGT​(p.Lys141SerfsTer17) 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: 16)
• Consequence: SLC28A1 NM_004213.5 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 7 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A1	NM_004213.5	MANE Select	c.419_420insGT	p.Lys141SerfsTer17	frameshift	Exon 6 of 19	NP_004204.3
	SLC28A1	NM_001287762.2		c.419_420insGT	p.Lys141SerfsTer17	frameshift	Exon 5 of 18	NP_001274691.1	O00337-1
	SLC28A1	NM_001321722.2		c.419_420insGT	p.Lys141SerfsTer17	frameshift	Exon 6 of 19	NP_001308651.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.419_420insGT	p.Lys141SerfsTer17	frameshift	Exon 6 of 19	ENSP00000378074.1	O00337-1
	SLC28A1	ENST00000286749.3	TSL:1	c.419_420insGT	p.Lys141SerfsTer17	frameshift	Exon 5 of 18	ENSP00000286749.3	O00337-1
	SLC28A1	ENST00000338602.6	TSL:1	c.419_420insGT	p.Lys141SerfsTer69	frameshift	Exon 6 of 7	ENSP00000341629.2	O00337-2

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17215836; hg19: chr15-85438311;