rs2236302
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_004995.4(MMP14):c.777C>A(p.Pro259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,814 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P259P) has been classified as Benign.
Frequency
Consequence
NM_004995.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP14 | NM_004995.4 | c.777C>A | p.Pro259= | synonymous_variant | 5/10 | ENST00000311852.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP14 | ENST00000311852.11 | c.777C>A | p.Pro259= | synonymous_variant | 5/10 | 1 | NM_004995.4 | P1 | |
MMP14 | ENST00000548162.2 | c.777C>A | p.Pro259= | synonymous_variant | 5/10 | 5 | |||
MMP14 | ENST00000680097.1 | c.*92C>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | |||||
MMP14 | ENST00000680941.1 | c.*175C>A | 3_prime_UTR_variant, NMD_transcript_variant | 6/11 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151996Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251318Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135842
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461818Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727208
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151996Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74244
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at