chr9-133537543-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_014694.4(ADAMTSL2):c.229C>T(p.Gln77Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_014694.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL2 | NM_014694.4 | c.229C>T | p.Gln77Ter | stop_gained | 3/19 | ENST00000651351.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL2 | ENST00000651351.2 | c.229C>T | p.Gln77Ter | stop_gained | 3/19 | NM_014694.4 | P1 | ||
ADAMTSL2 | ENST00000393061.7 | c.556C>T | p.Gln186Ter | stop_gained | 3/19 | 1 | |||
ADAMTSL2 | ENST00000354484.8 | c.229C>T | p.Gln77Ter | stop_gained | 3/19 | 1 | P1 | ||
ADAMTSL2 | ENST00000393060.1 | c.229C>T | p.Gln77Ter | stop_gained | 3/19 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1196016Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 576406
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
Lethal short-limb skeletal dysplasia, Al Gazali type Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Rare Disease Group, Clinical Genetics, Karolinska Institutet | Oct 11, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at