chr3-64540975-CCAATGTG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_182920.2(ADAMTS9):c.5521+113_5521+119del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 1,252,006 control chromosomes in the GnomAD database, including 396,062 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.64 ( 35502 hom., cov: 0)
Exomes 𝑓: 0.79 ( 360560 hom. )
Consequence
ADAMTS9
NM_182920.2 intron
NM_182920.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0890
Genes affected
ADAMTS9 (HGNC:13202): (ADAM metallopeptidase with thrombospondin type 1 motif 9) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS) motif. Individual members of this family differ in the number of C-terminal TS motifs, and some have unique C-terminal domains. Members of the ADAMTS family have been implicated in the cleavage of proteoglycans, the control of organ shape during development, and the inhibition of angiogenesis. This gene is localized to chromosome 3p14.3-p14.2, an area known to be lost in hereditary renal tumors. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 3-64540975-CCAATGTG-C is Benign according to our data. Variant chr3-64540975-CCAATGTG-C is described in ClinVar as [Benign]. Clinvar id is 1264037.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS9 | NM_182920.2 | c.5521+113_5521+119del | intron_variant | ENST00000498707.5 | |||
ADAMTS9 | NM_001318781.2 | c.5437+113_5437+119del | intron_variant | ||||
ADAMTS9 | XR_007095711.1 | n.5780+113_5780+119del | intron_variant, non_coding_transcript_variant | ||||
ADAMTS9 | XR_245151.1 | n.5864+113_5864+119del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS9 | ENST00000498707.5 | c.5521+113_5521+119del | intron_variant | 1 | NM_182920.2 | P1 | |||
ADAMTS9 | ENST00000295903.8 | c.5437+113_5437+119del | intron_variant | 1 | |||||
ADAMTS9 | ENST00000481060.2 | c.2688+113_2688+119del | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.641 AC: 96915AN: 151284Hom.: 35503 Cov.: 0
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GnomAD4 exome AF: 0.794 AC: 874399AN: 1100604Hom.: 360560 AF XY: 0.798 AC XY: 438205AN XY: 549202
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GnomAD4 genome ? AF: 0.640 AC: 96918AN: 151402Hom.: 35502 Cov.: 0 AF XY: 0.633 AC XY: 46749AN XY: 73910
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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 | GeneDx | May 08, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at