chr5-179128110-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014244.5(ADAMTS2):c.2466G>T(p.Pro822=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P822P) has been classified as Likely benign.
Frequency
Consequence
NM_014244.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS2 | NM_014244.5 | c.2466G>T | p.Pro822= | synonymous_variant | 17/22 | ENST00000251582.12 | |
ADAMTS2 | XM_047417895.1 | c.1971G>T | p.Pro657= | synonymous_variant | 16/21 | ||
ADAMTS2 | XM_047417896.1 | c.1584G>T | p.Pro528= | synonymous_variant | 15/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS2 | ENST00000251582.12 | c.2466G>T | p.Pro822= | synonymous_variant | 17/22 | 1 | NM_014244.5 | P2 | |
ADAMTS2 | ENST00000518335.3 | c.2466G>T | p.Pro822= | synonymous_variant | 17/21 | 3 | A2 | ||
ADAMTS2 | ENST00000698889.1 | c.2466G>T | p.Pro822= | synonymous_variant, NMD_transcript_variant | 17/21 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461212Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726914
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, dermatosparaxis type Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at