rs117187367
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014244.5(ADAMTS2):c.3506G>T(p.Gly1169Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000527 in 1,614,042 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014244.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS2 | NM_014244.5 | c.3506G>T | p.Gly1169Val | missense_variant | 22/22 | ENST00000251582.12 | |
ADAMTS2 | XM_047417895.1 | c.3011G>T | p.Gly1004Val | missense_variant | 21/21 | ||
ADAMTS2 | XM_047417896.1 | c.2624G>T | p.Gly875Val | missense_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS2 | ENST00000251582.12 | c.3506G>T | p.Gly1169Val | missense_variant | 22/22 | 1 | NM_014244.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000809 AC: 123AN: 152048Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00118 AC: 297AN: 251496Hom.: 3 AF XY: 0.000964 AC XY: 131AN XY: 135922
GnomAD4 exome AF: 0.000498 AC: 728AN: 1461876Hom.: 9 Cov.: 32 AF XY: 0.000461 AC XY: 335AN XY: 727234
GnomAD4 genome ? AF: 0.000808 AC: 123AN: 152166Hom.: 1 Cov.: 32 AF XY: 0.000887 AC XY: 66AN XY: 74390
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, dermatosparaxis type Benign:3
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
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 provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 04, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at