15-84904200-GTC-TTT

Variant names:

• chr15-84904200-GTC-TTT
• NM_004213.5:c.565_567delGTCinsTTT
• SLC28A1 p.Val189Phe

Variant summary

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

The NM_004213.5(SLC28A1):​c.565_567delGTCinsTTT​(p.Val189Phe) 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. V189I) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SLC28A1 NM_004213.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.79
• Publications: 0 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 0 ACMG points.

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.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	NP_004204.3
	SLC28A1	NM_001287762.2		c.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	NP_001274691.1	O00337-1
	SLC28A1	NM_001321722.2		c.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	NP_001308651.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	ENSP00000378074.1	O00337-1
	SLC28A1	ENST00000286749.3	TSL:1	c.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	ENSP00000286749.3	O00337-1
	SLC28A1	ENST00000859184.1		c.565_567delGTCinsTTT	p.Val189Phe	missense	N/A	ENSP00000529243.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.8

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: chr15-85447431;