Genetic Variant SLC28A1:p.Leu140_Lys141insIle (chr15-84895080-C-CTTA) – ACMG Classification: Uncertain_significance (3 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PM4_Supporting

The NM_004213.5(SLC28A1):c.419_420insTAT(p.Leu140_Lys141insIle) variant causes a disruptive inframe insertion 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.

Frequency

Genomes: not found (cov: 16)

Consequence

SLC28A1
NM_004213.5 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

7 publications found

Variant links:

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]

SLC28A1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_004213.5. Strenght limited to Supporting due to length of the change: 1aa.

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC28A1	NM_004213.5	MANE Select	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 19	NP_004204.3
SLC28A1	NM_001287762.2		c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 5 of 18	NP_001274691.1	O00337-1
SLC28A1	NM_001321722.2		c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 19	NP_001308651.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC28A1	ENST00000394573.6	TSL:1 MANE Select	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 19	ENSP00000378074.1	O00337-1
SLC28A1	ENST00000286749.3	TSL:1	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 5 of 18	ENSP00000286749.3	O00337-1
SLC28A1	ENST00000338602.6	TSL:1	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 7	ENSP00000341629.2	O00337-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

816

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over