chrX-108694921-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_033380.3(COL4A5):c.4821G>C(p.Met1607Ile) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar.
Frequency
Consequence
NM_033380.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.4821G>C | p.Met1607Ile | missense_variant, splice_region_variant | 51/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.4821G>C | p.Met1607Ile | missense_variant, splice_region_variant | 51/53 | 1 | NM_033380.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 24
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
X-linked Alport syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Medical Genetics, University of Parma | Mar 11, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at