15-84895080-CTC-TTG

Variant names:

• chr15-84895080-CTC-TTG
• NM_004213.5:c.418_420delCTCinsTTG
• SLC28A1 p.141

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_004213.5(SLC28A1):​c.418_420delCTCinsTTG​(p.141) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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.

• Frequency: Genomes: not found (cov: 16)
• Consequence: SLC28A1 NM_004213.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• 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: Likely_benign. The variant received -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=0.123 with no splicing effect.

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.418_420delCTCinsTTG	p.141	synonymous	N/A	NP_004204.3
	SLC28A1	NM_001287762.2		c.418_420delCTCinsTTG	p.141	synonymous	N/A	NP_001274691.1	O00337-1
	SLC28A1	NM_001321722.2		c.418_420delCTCinsTTG	p.141	synonymous	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.418_420delCTCinsTTG	p.141	synonymous	N/A	ENSP00000378074.1	O00337-1
	SLC28A1	ENST00000286749.3	TSL:1	c.418_420delCTCinsTTG	p.141	synonymous	N/A	ENSP00000286749.3	O00337-1
	SLC28A1	ENST00000338602.6	TSL:1	c.418_420delCTCinsTTG	p.141	synonymous	N/A	ENSP00000341629.2	O00337-2

Frequencies

GnomAD3 genomes Cov.: 16

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

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr15-85438311;