chr12-55837146-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002429.6(MMP19):c.1417C>T(p.Arg473Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,026 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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. R473G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002429.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP19 | NM_002429.6 | c.1417C>T | p.Arg473Cys | missense_variant | 9/9 | ENST00000322569.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP19 | ENST00000322569.9 | c.1417C>T | p.Arg473Cys | missense_variant | 9/9 | 1 | NM_002429.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152174Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251428Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135884
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461852Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727234
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152174Hom.: 1 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1417C>T (p.R473C) alteration is located in exon 9 (coding exon 9) of the MMP19 gene. This alteration results from a C to T substitution at nucleotide position 1417, causing the arginine (R) at amino acid position 473 to be replaced by a cysteine (C). 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