8-17561952-GTG-CTT

Variant names:

• chr8-17561952-GTG-CTT
• NM_001370338.1:c.1513_1515delGTGinsCTT
• SLC7A2 p.Val505Leu

Variant summary

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

The NM_001370338.1(SLC7A2):​c.1513_1515delGTGinsCTT​(p.Val505Leu) variant causes a missense change involving the alteration of a conserved nucleotide. 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC7A2 NM_001370338.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.34
• Publications: 0 publications found

Genes affected

SLC7A2 (HGNC:11060): (solute carrier family 7 member 2) The protein encoded by this gene is a cationic amino acid transporter and a member of the APC (amino acid-polyamine-organocation) family of transporters. The encoded membrane protein is responsible for the cellular uptake of arginine, lysine and ornithine. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370338.1. 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
	SLC7A2	NM_001370338.1	MANE Select	c.1513_1515delGTGinsCTT	p.Val505Leu	missense	N/A	NP_001357267.1	P52569-1
	SLC7A2	NM_001164771.2		c.1633_1635delGTGinsCTT	p.Val545Leu	missense	N/A	NP_001158243.1	P52569-3
	SLC7A2	NM_003046.6		c.1630_1632delGTGinsCTT	p.Val544Leu	missense	N/A	NP_003037.4	P52569-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC7A2	ENST00000494857.6	TSL:5 MANE Select	c.1513_1515delGTGinsCTT	p.Val505Leu	missense	N/A	ENSP00000419140.2	P52569-1
	SLC7A2	ENST00000004531.14	TSL:1	c.1633_1635delGTGinsCTT	p.Val545Leu	missense	N/A	ENSP00000004531.10	P52569-3
	SLC7A2	ENST00000398090.3	TSL:1	c.1630_1632delGTGinsCTT	p.Val544Leu	missense	N/A	ENSP00000381164.3	P52569-2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.3

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: chr8-17419461;