19-50909059-A-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004917.5(KLK4):c.224+193T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000754 in 1,326,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_004917.5 intron
Scores
Clinical Significance
Conservation
Publications
- amelogenesis imperfecta type 2A1Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- amelogenesis imperfecta type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KLK4 | NM_004917.5 | c.224+193T>A | intron_variant | Intron 3 of 5 | ENST00000324041.6 | NP_004908.4 | ||
KLK4 | NM_001302961.2 | c.-62+181T>A | intron_variant | Intron 2 of 4 | NP_001289890.1 | |||
KLK4 | NR_126566.2 | n.217+181T>A | intron_variant | Intron 2 of 4 | ||||
KLK4 | XM_011527545.4 | c.224+193T>A | intron_variant | Intron 2 of 3 | XP_011525847.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLK4 | ENST00000324041.6 | c.224+193T>A | intron_variant | Intron 3 of 5 | 1 | NM_004917.5 | ENSP00000326159.1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 7.54e-7 AC: 1AN: 1326400Hom.: 0 Cov.: 40 AF XY: 0.00 AC XY: 0AN XY: 646626 show subpopulations
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at