3-64686858-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182920.2(ADAMTS9):āc.226A>Gā(p.Ile76Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,614,130 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_182920.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTS9 | NM_182920.2 | c.226A>G | p.Ile76Val | missense_variant | 2/40 | ENST00000498707.5 | NP_891550.1 | |
ADAMTS9-AS2 | NR_038264.1 | n.469+1520T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTS9 | ENST00000498707.5 | c.226A>G | p.Ile76Val | missense_variant | 2/40 | 1 | NM_182920.2 | ENSP00000418735 | P1 | |
ADAMTS9-AS2 | ENST00000650103.1 | n.404+1520T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00569 AC: 865AN: 152124Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00171 AC: 429AN: 251400Hom.: 5 AF XY: 0.00139 AC XY: 189AN XY: 135872
GnomAD4 exome AF: 0.000568 AC: 830AN: 1461890Hom.: 5 Cov.: 32 AF XY: 0.000496 AC XY: 361AN XY: 727246
GnomAD4 genome AF: 0.00567 AC: 863AN: 152240Hom.: 12 Cov.: 33 AF XY: 0.00540 AC XY: 402AN XY: 74428
ClinVar
Submissions by phenotype
ADAMTS9-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 14, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at