16-58039997-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002428.4(MMP15):c.563G>A(p.Arg188Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,952 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. R188W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002428.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP15 | NM_002428.4 | c.563G>A | p.Arg188Gln | missense_variant | 4/10 | ENST00000219271.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP15 | ENST00000219271.4 | c.563G>A | p.Arg188Gln | missense_variant | 4/10 | 1 | NM_002428.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152282Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251098Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135848
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461670Hom.: 1 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727142
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.563G>A (p.R188Q) alteration is located in exon 4 (coding exon 4) of the MMP15 gene. This alteration results from a G to A substitution at nucleotide position 563, causing the arginine (R) at amino acid position 188 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