chr19-8586678-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_030957.4(ADAMTS10):āc.2283T>Cā(p.Pro761=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,613,782 control chromosomes in the GnomAD database, including 37,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P761P) has been classified as Likely benign.
Frequency
Consequence
NM_030957.4 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 |
---|---|---|---|---|---|---|---|
ADAMTS10 | NM_030957.4 | c.2283T>C | p.Pro761= | synonymous_variant | 20/26 | ENST00000597188.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS10 | ENST00000597188.6 | c.2283T>C | p.Pro761= | synonymous_variant | 20/26 | 5 | NM_030957.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.220 AC: 33350AN: 151868Hom.: 3740 Cov.: 32
GnomAD3 exomes AF: 0.213 AC: 53351AN: 250704Hom.: 6042 AF XY: 0.207 AC XY: 28055AN XY: 135750
GnomAD4 exome AF: 0.212 AC: 310219AN: 1461794Hom.: 33671 Cov.: 36 AF XY: 0.210 AC XY: 152699AN XY: 727214
GnomAD4 genome AF: 0.220 AC: 33369AN: 151988Hom.: 3738 Cov.: 32 AF XY: 0.220 AC XY: 16356AN XY: 74288
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2018 | 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. - |
Weill-Marchesani syndrome Benign:1
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at