chr12-43383877-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025003.5(ADAMTS20):c.4553G>A(p.Arg1518Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025003.5 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 |
---|---|---|---|---|---|---|---|
ADAMTS20 | NM_025003.5 | c.4553G>A | p.Arg1518Gln | missense_variant | 30/39 | ENST00000389420.8 | |
ADAMTS20 | XM_011538754.3 | c.4556G>A | p.Arg1519Gln | missense_variant | 30/39 | ||
ADAMTS20 | XM_017019979.2 | c.3341G>A | p.Arg1114Gln | missense_variant | 23/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS20 | ENST00000389420.8 | c.4553G>A | p.Arg1518Gln | missense_variant | 30/39 | 1 | NM_025003.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250982Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135646
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461670Hom.: 0 Cov.: 32 AF XY: 0.0000481 AC XY: 35AN XY: 727126
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2023 | The c.4553G>A (p.R1518Q) alteration is located in exon 30 (coding exon 30) of the ADAMTS20 gene. This alteration results from a G to A substitution at nucleotide position 4553, causing the arginine (R) at amino acid position 1518 to be replaced by a glutamine (Q). 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