5-179345258-GGCAGCAGCAGCA-GGCAGCAGCAGCAGCAGCA
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_014244.5(ADAMTS2):c.65_70dupTGCTGC(p.Leu22_Leu23dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000253 in 1,136,418 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014244.5 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAMTS2 | NM_014244.5 | c.65_70dupTGCTGC | p.Leu22_Leu23dup | conservative_inframe_insertion | Exon 1 of 22 | ENST00000251582.12 | NP_055059.2 | |
ADAMTS2 | NM_021599.4 | c.65_70dupTGCTGC | p.Leu22_Leu23dup | conservative_inframe_insertion | Exon 1 of 11 | NP_067610.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTS2 | ENST00000251582.12 | c.65_70dupTGCTGC | p.Leu22_Leu23dup | conservative_inframe_insertion | Exon 1 of 22 | 1 | NM_014244.5 | ENSP00000251582.7 | ||
ADAMTS2 | ENST00000274609.5 | c.65_70dupTGCTGC | p.Leu22_Leu23dup | conservative_inframe_insertion | Exon 1 of 11 | 1 | ENSP00000274609.5 | |||
ADAMTS2 | ENST00000518335.3 | c.65_70dupTGCTGC | p.Leu22_Leu23dup | conservative_inframe_insertion | Exon 1 of 21 | 3 | ENSP00000489888.2 | |||
ADAMTS2 | ENST00000698889.1 | n.65_70dupTGCTGC | non_coding_transcript_exon_variant | Exon 1 of 21 | ENSP00000514008.1 |
Frequencies
GnomAD3 genomes AF: 0.000408 AC: 60AN: 146978Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.000896 AC: 1AN: 1116Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 680
GnomAD4 exome AF: 0.000229 AC: 227AN: 989348Hom.: 0 Cov.: 29 AF XY: 0.000261 AC XY: 123AN XY: 472142
GnomAD4 genome AF: 0.000415 AC: 61AN: 147070Hom.: 0 Cov.: 28 AF XY: 0.000251 AC XY: 18AN XY: 71648
ClinVar
Submissions by phenotype
not provided Benign:2
See Variant Classification Assertion Criteria. -
ADAMTS2: BS2 -
Ehlers-Danlos syndrome, dermatosparaxis type Uncertain:1
This variant, c.65_70dup, results in the insertion of 2 amino acid(s) of the ADAMTS2 protein (p.Leu22_Leu23dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with ADAMTS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 506736). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Ehlers-Danlos syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at