rs3751489
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004995.4(MMP14):c.1292G>A(p.Arg431His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000554 in 1,614,050 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts 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_004995.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP14 | NM_004995.4 | c.1292G>A | p.Arg431His | missense_variant | 8/10 | ENST00000311852.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP14 | ENST00000311852.11 | c.1292G>A | p.Arg431His | missense_variant | 8/10 | 1 | NM_004995.4 | P1 | |
MMP14 | ENST00000548162.2 | c.1292G>A | p.Arg431His | missense_variant | 8/10 | 5 | |||
MMP14 | ENST00000680097.1 | c.*607G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/10 | |||||
MMP14 | ENST00000680941.1 | c.*690G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/11 |
Frequencies
GnomAD3 genomes ? AF: 0.000776 AC: 118AN: 152094Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00182 AC: 458AN: 251424Hom.: 3 AF XY: 0.00160 AC XY: 218AN XY: 135894
GnomAD4 exome AF: 0.000531 AC: 776AN: 1461838Hom.: 5 Cov.: 32 AF XY: 0.000545 AC XY: 396AN XY: 727220
GnomAD4 genome ? AF: 0.000775 AC: 118AN: 152212Hom.: 1 Cov.: 32 AF XY: 0.000860 AC XY: 64AN XY: 74438
ClinVar
Submissions by phenotype
MMP14-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 13, 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at