rs386833817
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_StrongPM2PP3_Strong
The NM_003982.4(SLC7A7):c.499+1G>C variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003982.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC7A7 | NM_003982.4 | c.499+1G>C | splice_donor_variant | ENST00000674313.1 | |||
SLC7A7 | NM_001126105.3 | c.499+1G>C | splice_donor_variant | ||||
SLC7A7 | NM_001126106.4 | c.499+1G>C | splice_donor_variant | ||||
SLC7A7 | XM_011537299.2 | c.499+1G>C | splice_donor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC7A7 | ENST00000674313.1 | c.499+1G>C | splice_donor_variant | NM_003982.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151706Hom.: 0 Cov.: 29
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461156Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 726858
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151706Hom.: 0 Cov.: 29 AF XY: 0.0000270 AC XY: 2AN XY: 74086
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at