X-108539746-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_033380.3(COL4A5):c.82G>T(p.Ala28Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/24 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A28T) has been classified as Uncertain significance.
Frequency
Consequence
NM_033380.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.82G>T | p.Ala28Ser | missense_variant, splice_region_variant | 2/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.82G>T | p.Ala28Ser | missense_variant, splice_region_variant | 2/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000361603.7 | c.82G>T | p.Ala28Ser | missense_variant, splice_region_variant | 2/51 | 2 | P1 | ||
COL4A5 | ENST00000470339.1 | n.266G>T | splice_region_variant, non_coding_transcript_exon_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
X-linked Alport syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Diagnostic Laboratory, University of Szeged | Feb 02, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at