14-22787413-G-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003982.4(SLC7A7):c.500-7362C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 29)
Failed GnomAD Quality Control
Consequence
SLC7A7
NM_003982.4 intron
NM_003982.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.123
Genes affected
SLC7A7 (HGNC:11065): (solute carrier family 7 member 7) The protein encoded by this gene is the light subunit of a cationic amino acid transporter. This sodium-independent transporter is formed when the light subunit encoded by this gene dimerizes with the heavy subunit transporter protein SLC3A2. This transporter is found in epithelial cell membranes where it transfers cationic and large neutral amino acids from the cell to the extracellular space. Defects in this gene are a cause of lysinuric protein intolerance (LPI). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A7 | NM_003982.4 | c.500-7362C>G | intron_variant | Intron 2 of 9 | ENST00000674313.1 | NP_003973.3 | ||
SLC7A7 | NM_001126105.3 | c.500-7362C>G | intron_variant | Intron 3 of 10 | NP_001119577.1 | |||
SLC7A7 | NM_001126106.4 | c.500-7362C>G | intron_variant | Intron 3 of 10 | NP_001119578.1 | |||
SLC7A7 | XM_011537299.2 | c.500-7362C>G | intron_variant | Intron 2 of 9 | XP_011535601.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150946Hom.: 0 Cov.: 29 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 150946Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 73628
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at