5-179114023-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014244.5(ADAMTS2):c.3480C>A(p.Ala1160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0019 in 1,614,108 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A1160A) has been classified as Uncertain significance.
Frequency
Consequence
NM_014244.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS2 | NM_014244.5 | c.3480C>A | p.Ala1160= | synonymous_variant | 22/22 | ENST00000251582.12 | |
ADAMTS2 | XM_047417895.1 | c.2985C>A | p.Ala995= | synonymous_variant | 21/21 | ||
ADAMTS2 | XM_047417896.1 | c.2598C>A | p.Ala866= | synonymous_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS2 | ENST00000251582.12 | c.3480C>A | p.Ala1160= | synonymous_variant | 22/22 | 1 | NM_014244.5 | P2 | |
ADAMTS2 | ENST00000522937.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00992 AC: 1509AN: 152096Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.00247 AC: 622AN: 251496Hom.: 9 AF XY: 0.00172 AC XY: 234AN XY: 135922
GnomAD4 exome AF: 0.00105 AC: 1542AN: 1461894Hom.: 35 Cov.: 32 AF XY: 0.000888 AC XY: 646AN XY: 727248
GnomAD4 genome AF: 0.00997 AC: 1518AN: 152214Hom.: 24 Cov.: 32 AF XY: 0.00942 AC XY: 701AN XY: 74420
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, dermatosparaxis type Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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 | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
ADAMTS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 20, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at