chr12-55837124-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002429.6(MMP19):c.1439C>A(p.Thr480Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000156 in 1,613,856 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T480A) has been classified as Uncertain significance.
Frequency
Consequence
NM_002429.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP19 | NM_002429.6 | c.1439C>A | p.Thr480Asn | missense_variant | 9/9 | ENST00000322569.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP19 | ENST00000322569.9 | c.1439C>A | p.Thr480Asn | missense_variant | 9/9 | 1 | NM_002429.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 76AN: 251160Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135726
GnomAD4 exome AF: 0.000153 AC: 224AN: 1461634Hom.: 0 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 727104
GnomAD4 genome AF: 0.000177 AC: 27AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.1439C>A (p.T480N) alteration is located in exon 9 (coding exon 9) of the MMP19 gene. This alteration results from a C to A substitution at nucleotide position 1439, causing the threonine (T) at amino acid position 480 to be replaced by an asparagine (N). 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