chr15-78764041-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014272.5(ADAMTS7):c.4478G>A(p.Arg1493Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000448 in 1,539,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014272.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS7 | NM_014272.5 | c.4478G>A | p.Arg1493Gln | missense_variant | 21/24 | ENST00000388820.5 | |
ADAMTS7 | XM_047432122.1 | c.4478G>A | p.Arg1493Gln | missense_variant | 21/24 | ||
ADAMTS7 | XM_047432123.1 | c.3719G>A | p.Arg1240Gln | missense_variant | 20/23 | ||
ADAMTS7 | XM_011521166.3 | c.2732G>A | p.Arg911Gln | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS7 | ENST00000388820.5 | c.4478G>A | p.Arg1493Gln | missense_variant | 21/24 | 1 | NM_014272.5 | P1 | |
ADAMTS7 | ENST00000569934.1 | n.618G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000820 AC: 12AN: 146276Hom.: 0 AF XY: 0.000116 AC XY: 9AN XY: 77706
GnomAD4 exome AF: 0.0000461 AC: 64AN: 1386984Hom.: 0 Cov.: 31 AF XY: 0.0000644 AC XY: 44AN XY: 682942
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152262Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.4478G>A (p.R1493Q) alteration is located in exon 21 (coding exon 21) of the ADAMTS7 gene. This alteration results from a G to A substitution at nucleotide position 4478, causing the arginine (R) at amino acid position 1493 to be replaced by a glutamine (Q). 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