chr12-43369297-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_025003.5(ADAMTS20):c.5531G>A(p.Cys1844Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000331 in 1,512,816 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 Uncertain significance (★).
Frequency
Consequence
NM_025003.5 missense
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 |
---|---|---|---|---|---|---|---|---|
ADAMTS20 | NM_025003.5 | c.5531G>A | p.Cys1844Tyr | missense_variant | Exon 37 of 39 | ENST00000389420.8 | NP_079279.3 | |
ADAMTS20 | XM_011538754.3 | c.5534G>A | p.Cys1845Tyr | missense_variant | Exon 37 of 39 | XP_011537056.1 | ||
ADAMTS20 | XM_017019979.2 | c.4319G>A | p.Cys1440Tyr | missense_variant | Exon 30 of 32 | XP_016875468.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151952Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 176562Hom.: 0 AF XY: 0.0000105 AC XY: 1AN XY: 95684
GnomAD4 exome AF: 0.00000294 AC: 4AN: 1360864Hom.: 0 Cov.: 28 AF XY: 0.00000297 AC XY: 2AN XY: 673866
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151952Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5531G>A (p.C1844Y) alteration is located in exon 37 (coding exon 37) of the ADAMTS20 gene. This alteration results from a G to A substitution at nucleotide position 5531, causing the cysteine (C) at amino acid position 1844 to be replaced by a tyrosine (Y). 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