chr3-64550972-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_182920.2(ADAMTS9):c.4789G>A(p.Val1597Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,614,210 control chromosomes in the GnomAD database, including 57 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 (★★).
Frequency
Consequence
NM_182920.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS9 | NM_182920.2 | c.4789G>A | p.Val1597Met | missense_variant | 31/40 | ENST00000498707.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS9 | ENST00000498707.5 | c.4789G>A | p.Val1597Met | missense_variant | 31/40 | 1 | NM_182920.2 | P1 | |
ADAMTS9 | ENST00000295903.8 | c.4705G>A | p.Val1569Met | missense_variant | 30/39 | 1 | |||
ADAMTS9 | ENST00000482490.5 | n.4316G>A | non_coding_transcript_exon_variant | 30/30 | 1 | ||||
ADAMTS9 | ENST00000481060.2 | c.1957G>A | p.Val653Met | missense_variant | 12/21 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00173 AC: 263AN: 152210Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00323 AC: 812AN: 251416Hom.: 16 AF XY: 0.00292 AC XY: 397AN XY: 135868
GnomAD4 exome AF: 0.00137 AC: 1997AN: 1461880Hom.: 51 Cov.: 30 AF XY: 0.00130 AC XY: 945AN XY: 727244
GnomAD4 genome ? AF: 0.00172 AC: 262AN: 152330Hom.: 6 Cov.: 32 AF XY: 0.00191 AC XY: 142AN XY: 74472
ClinVar
Submissions by phenotype
ADAMTS9-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 23, 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 | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at