chr15-84895080-C-CTTA

Variant names:

• chr15-84895080-C-CTTA
• rs17215836
• NM_004213.5:c.419_420insTAT

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PM4_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
• 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 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC28A1	NM_004213.5	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 19	ENST00000394573.6	NP_004204.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC28A1	ENST00000394573.6	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 19	1	NM_004213.5	ENSP00000378074.1
SLC28A1	ENST00000286749.3	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 5 of 18	1		ENSP00000286749.3
SLC28A1	ENST00000338602.6	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 6 of 7	1		ENSP00000341629.2
SLC28A1	ENST00000538177.5	c.419_420insTAT	p.Leu140_Lys141insIle	disruptive_inframe_insertion	Exon 5 of 15	2		ENSP00000443752.1

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 16

Alfa AF: 0.00 Hom.: 816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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;