12-43376634-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025003.5(ADAMTS20):āc.5015T>Cā(p.Ile1672Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000288 in 1,612,568 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS20 | NM_025003.5 | c.5015T>C | p.Ile1672Thr | missense_variant | 33/39 | ENST00000389420.8 | |
ADAMTS20 | XM_011538754.3 | c.5018T>C | p.Ile1673Thr | missense_variant | 33/39 | ||
ADAMTS20 | XM_017019979.2 | c.3803T>C | p.Ile1268Thr | missense_variant | 26/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS20 | ENST00000389420.8 | c.5015T>C | p.Ile1672Thr | missense_variant | 33/39 | 1 | NM_025003.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000209 AC: 52AN: 249292Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134714
GnomAD4 exome AF: 0.000297 AC: 433AN: 1460366Hom.: 1 Cov.: 31 AF XY: 0.000301 AC XY: 219AN XY: 726404
GnomAD4 genome AF: 0.000204 AC: 31AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.5015T>C (p.I1672T) alteration is located in exon 33 (coding exon 33) of the ADAMTS20 gene. This alteration results from a T to C substitution at nucleotide position 5015, causing the isoleucine (I) at amino acid position 1672 to be replaced by a threonine (T). 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