chr12-131828520-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016155.7(MMP17):c.26C>A(p.Pro9His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 995,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. P9A) has been classified as Uncertain significance.
Frequency
Consequence
NM_016155.7 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 |
---|---|---|---|---|---|---|---|
MMP17 | NM_016155.7 | c.26C>A | p.Pro9His | missense_variant | 1/10 | ENST00000360564.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP17 | ENST00000360564.5 | c.26C>A | p.Pro9His | missense_variant | 1/10 | 1 | NM_016155.7 | P1 | |
MMP17 | ENST00000535004.2 | c.26C>A | p.Pro9His | missense_variant, NMD_transcript_variant | 1/10 | 3 | |||
MMP17 | ENST00000545790.6 | c.26C>A | p.Pro9His | missense_variant, NMD_transcript_variant | 1/11 | 2 | |||
MMP17 | ENST00000545671.6 | c.26C>A | p.Pro9His | missense_variant, NMD_transcript_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000685 AC: 10AN: 146038Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.000140 AC: 119AN: 849756Hom.: 0 Cov.: 29 AF XY: 0.000114 AC XY: 45AN XY: 394522
GnomAD4 genome ? AF: 0.0000685 AC: 10AN: 146038Hom.: 0 Cov.: 34 AF XY: 0.0000563 AC XY: 4AN XY: 71028
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.26C>A (p.P9H) alteration is located in exon 1 (coding exon 1) of the MMP17 gene. This alteration results from a C to A substitution at nucleotide position 26, causing the proline (P) at amino acid position 9 to be replaced by a histidine (H). 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