12-55837101-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002429.6(MMP19):c.1462C>A(p.Pro488Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,611,638 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002429.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP19 | NM_002429.6 | c.1462C>A | p.Pro488Thr | missense_variant | 9/9 | ENST00000322569.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP19 | ENST00000322569.9 | c.1462C>A | p.Pro488Thr | missense_variant | 9/9 | 1 | NM_002429.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0113 AC: 1719AN: 152154Hom.: 35 Cov.: 32
GnomAD3 exomes AF: 0.00307 AC: 766AN: 249630Hom.: 14 AF XY: 0.00234 AC XY: 315AN XY: 134828
GnomAD4 exome AF: 0.00127 AC: 1848AN: 1459366Hom.: 30 Cov.: 31 AF XY: 0.00113 AC XY: 823AN XY: 725680
GnomAD4 genome AF: 0.0113 AC: 1719AN: 152272Hom.: 35 Cov.: 32 AF XY: 0.0110 AC XY: 819AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at