chr21-45504504-GC-G
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1
The NM_001379500.1(COL18A1):c.2823del(p.Gly942AlafsTer89) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000194 in 1,392,616 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G939G) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001379500.1 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.2823del | p.Gly942AlafsTer89 | frameshift_variant | 34/42 | ENST00000651438.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.2823del | p.Gly942AlafsTer89 | frameshift_variant | 34/42 | NM_001379500.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00125 AC: 4AN: 3200Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000360 AC: 2AN: 55592Hom.: 0 AF XY: 0.0000638 AC XY: 2AN XY: 31350
GnomAD4 exome AF: 0.0000166 AC: 23AN: 1389416Hom.: 0 Cov.: 30 AF XY: 0.0000174 AC XY: 12AN XY: 690766
GnomAD4 genome ? AF: 0.00125 AC: 4AN: 3200Hom.: 0 Cov.: 29 AF XY: 0.00193 AC XY: 3AN XY: 1552
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at