21-26924148-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_007038.5(ADAMTS5):c.2698G>A(p.Val900Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007038.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAMTS5 | ENST00000284987.6 | c.2698G>A | p.Val900Met | missense_variant | Exon 8 of 8 | 1 | NM_007038.5 | ENSP00000284987.5 | ||
ADAMTS5 | ENST00000652031.1 | n.*1429G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | ENSP00000498989.1 | |||||
ADAMTS5 | ENST00000652031.1 | n.*1429G>A | 3_prime_UTR_variant | Exon 9 of 9 | ENSP00000498989.1 | |||||
ENSG00000223563 | ENST00000426771.1 | n.234+14118C>T | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251064Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135660
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461670Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727092
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2698G>A (p.V900M) alteration is located in exon 8 (coding exon 8) of the ADAMTS5 gene. This alteration results from a G to A substitution at nucleotide position 2698, causing the valine (V) at amino acid position 900 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at