chr14-22843345-C-G
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_004995.4(MMP14):c.777C>G(p.Pro259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,613,690 control chromosomes in the GnomAD database, including 11,861 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P259P) has been classified as Likely benign.
Frequency
Consequence
NM_004995.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP14 | NM_004995.4 | c.777C>G | 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>G | p.Pro259= | synonymous_variant | 5/10 | 1 | NM_004995.4 | P1 | |
MMP14 | ENST00000548162.2 | c.777C>G | p.Pro259= | synonymous_variant | 5/10 | 5 | |||
MMP14 | ENST00000680097.1 | c.*92C>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | |||||
MMP14 | ENST00000680941.1 | c.*175C>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/11 |
Frequencies
GnomAD3 genomes ? AF: 0.158 AC: 23971AN: 151940Hom.: 2355 Cov.: 31
GnomAD3 exomes AF: 0.123 AC: 30878AN: 251318Hom.: 2269 AF XY: 0.116 AC XY: 15766AN XY: 135842
GnomAD4 exome AF: 0.109 AC: 159160AN: 1461632Hom.: 9501 Cov.: 32 AF XY: 0.107 AC XY: 77940AN XY: 727110
GnomAD4 genome ? AF: 0.158 AC: 23998AN: 152058Hom.: 2360 Cov.: 31 AF XY: 0.156 AC XY: 11579AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
MMP14-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at