rs3118667
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_139027.6(ADAMTS13):āc.420T>Cā(p.Ala140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 1,613,002 control chromosomes in the GnomAD database, including 182,900 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.47 ( 17440 hom., cov: 32)
Exomes š: 0.47 ( 165460 hom. )
Consequence
ADAMTS13
NM_139027.6 synonymous
NM_139027.6 synonymous
Scores
1
Clinical Significance
Conservation
PhyloP100: 0.339
Genes affected
ADAMTS13 (HGNC:1366): (ADAM metallopeptidase with thrombospondin type 1 motif 13) This gene encodes a member of a family of proteins containing several distinct regions, including a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. The enzyme encoded by this gene specifically cleaves von Willebrand Factor (vWF). Defects in this gene are associated with thrombotic thrombocytopenic purpura. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 9-133425943-T-C is Benign according to our data. Variant chr9-133425943-T-C is described in ClinVar as [Benign]. Clinvar id is 769358.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.339 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS13 | NM_139027.6 | c.420T>C | p.Ala140= | synonymous_variant | 5/29 | ENST00000355699.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS13 | ENST00000355699.7 | c.420T>C | p.Ala140= | synonymous_variant | 5/29 | 1 | NM_139027.6 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.471 AC: 71558AN: 151850Hom.: 17411 Cov.: 32
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GnomAD4 exome AF: 0.471 AC: 687479AN: 1461034Hom.: 165460 Cov.: 82 AF XY: 0.471 AC XY: 341951AN XY: 726778
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GnomAD4 genome ? AF: 0.471 AC: 71634AN: 151968Hom.: 17440 Cov.: 32 AF XY: 0.472 AC XY: 35045AN XY: 74278
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at