rs28567966
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_139057.4(ADAMTS17):āc.1445T>Cā(p.Met482Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,613,936 control chromosomes in the GnomAD database, including 18,976 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_139057.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTS17 | NM_139057.4 | c.1445T>C | p.Met482Thr | missense_variant | 10/22 | ENST00000268070.9 | NP_620688.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTS17 | ENST00000268070.9 | c.1445T>C | p.Met482Thr | missense_variant | 10/22 | 1 | NM_139057.4 | ENSP00000268070.4 | ||
ADAMTS17 | ENST00000568565.2 | c.1445T>C | p.Met482Thr | missense_variant | 10/23 | 5 | ENSP00000456161.2 | |||
ADAMTS17 | ENST00000378898.8 | n.1126T>C | non_coding_transcript_exon_variant | 9/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.156 AC: 23663AN: 152016Hom.: 2008 Cov.: 32
GnomAD3 exomes AF: 0.141 AC: 35439AN: 251380Hom.: 2855 AF XY: 0.145 AC XY: 19744AN XY: 135862
GnomAD4 exome AF: 0.148 AC: 216343AN: 1461802Hom.: 16961 Cov.: 41 AF XY: 0.150 AC XY: 109272AN XY: 727202
GnomAD4 genome AF: 0.156 AC: 23694AN: 152134Hom.: 2015 Cov.: 32 AF XY: 0.152 AC XY: 11322AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Weill-Marchesani 4 syndrome, recessive Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at