rs3918254
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004994.3(MMP9):c.997+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0129 in 1,609,020 control chromosomes in the GnomAD database, including 1,269 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004994.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP9 | NM_004994.3 | c.997+5C>T | splice_donor_5th_base_variant, intron_variant | ENST00000372330.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP9 | ENST00000372330.3 | c.997+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_004994.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0281 AC: 4273AN: 152096Hom.: 218 Cov.: 33
GnomAD3 exomes AF: 0.0298 AC: 7250AN: 243486Hom.: 458 AF XY: 0.0278 AC XY: 3678AN XY: 132258
GnomAD4 exome AF: 0.0113 AC: 16425AN: 1456806Hom.: 1051 Cov.: 36 AF XY: 0.0115 AC XY: 8343AN XY: 724836
GnomAD4 genome ? AF: 0.0281 AC: 4275AN: 152214Hom.: 218 Cov.: 33 AF XY: 0.0298 AC XY: 2218AN XY: 74422
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2019 | - - |
Metaphyseal anadysplasia 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at