16-55479584-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6BP7BS1
The NM_004530.6(MMP2):c.105C>T(p.Ile35Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004530.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP2 | NM_004530.6 | c.105C>T | p.Ile35Ile | synonymous_variant | Exon 1 of 13 | ENST00000219070.9 | NP_004521.1 | |
MMP2 | NM_001302508.1 | c.-76+619C>T | intron_variant | Intron 1 of 12 | NP_001289437.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP2 | ENST00000219070.9 | c.105C>T | p.Ile35Ile | synonymous_variant | Exon 1 of 13 | 1 | NM_004530.6 | ENSP00000219070.4 | ||
MMP2 | ENST00000570308.5 | c.-75-3325C>T | intron_variant | Intron 2 of 13 | 1 | ENSP00000461421.1 | ||||
MMP2 | ENST00000568715.5 | c.-76+619C>T | intron_variant | Intron 1 of 3 | 4 | ENSP00000457949.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249572Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135486
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461358Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 726990
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at