rs1357144982
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_000174.5(GP9):c.-13+2T>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000241 in 831,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 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_000174.5 splice_donor, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GP9 | NM_000174.5 | c.-13+2T>A | splice_donor_variant, intron_variant | Intron 2 of 2 | ENST00000307395.5 | NP_000165.1 | ||
GP9 | XM_047447997.1 | c.-12-107T>A | intron_variant | Intron 1 of 1 | XP_047303953.1 | |||
GP9 | XM_005247374.4 | c.*84T>A | downstream_gene_variant | XP_005247431.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151768Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000147 AC: 1AN: 679266Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0AN XY: 358050
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151768Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74100
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at