chr15-83820010-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_207517.3(ADAMTSL3):c.563C>T(p.Thr188Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000855 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207517.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.563C>T | p.Thr188Met | missense_variant | 6/30 | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.563C>T | p.Thr188Met | missense_variant | 6/30 | 1 | NM_207517.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251436Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135888
GnomAD4 exome AF: 0.0000841 AC: 123AN: 1461882Hom.: 0 Cov.: 34 AF XY: 0.0000756 AC XY: 55AN XY: 727242
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.563C>T (p.T188M) alteration is located in exon 6 (coding exon 5) of the ADAMTSL3 gene. This alteration results from a C to T substitution at nucleotide position 563, causing the threonine (T) at amino acid position 188 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at