15-78763839-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014272.5(ADAMTS7):c.4600G>A(p.Glu1534Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,582,604 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1534D) has been classified as Uncertain significance.
Frequency
Consequence
NM_014272.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS7 | NM_014272.5 | c.4600G>A | p.Glu1534Lys | missense_variant | 22/24 | ENST00000388820.5 | |
ADAMTS7 | XM_047432122.1 | c.4600G>A | p.Glu1534Lys | missense_variant | 22/24 | ||
ADAMTS7 | XM_047432123.1 | c.3841G>A | p.Glu1281Lys | missense_variant | 21/23 | ||
ADAMTS7 | XM_011521166.3 | c.2854G>A | p.Glu952Lys | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS7 | ENST00000388820.5 | c.4600G>A | p.Glu1534Lys | missense_variant | 22/24 | 1 | NM_014272.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000203 AC: 4AN: 196674Hom.: 0 AF XY: 0.0000280 AC XY: 3AN XY: 107140
GnomAD4 exome AF: 0.0000112 AC: 16AN: 1430338Hom.: 1 Cov.: 31 AF XY: 0.0000169 AC XY: 12AN XY: 709144
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152266Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 05, 2023 | The c.4600G>A (p.E1534K) alteration is located in exon 22 (coding exon 22) of the ADAMTS7 gene. This alteration results from a G to A substitution at nucleotide position 4600, causing the glutamic acid (E) at amino acid position 1534 to be replaced by a lysine (K). 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