chr12-43383959-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025003.5(ADAMTS20):āc.4471T>Cā(p.Ser1491Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.4471T>C | p.Ser1491Pro | missense_variant | 30/39 | ENST00000389420.8 | |
ADAMTS20 | XM_011538754.3 | c.4474T>C | p.Ser1492Pro | missense_variant | 30/39 | ||
ADAMTS20 | XM_017019979.2 | c.3259T>C | p.Ser1087Pro | missense_variant | 23/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS20 | ENST00000389420.8 | c.4471T>C | p.Ser1491Pro | missense_variant | 30/39 | 1 | NM_025003.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250494Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135332
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461484Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727008
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.4471T>C (p.S1491P) alteration is located in exon 30 (coding exon 30) of the ADAMTS20 gene. This alteration results from a T to C substitution at nucleotide position 4471, causing the serine (S) at amino acid position 1491 to be replaced by a proline (P). 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