X-108584530-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_033380.3(COL4A5):c.1032+5G>T variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.0000023 in 870,157 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033380.3 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.1032+5G>T | splice_donor_5th_base_variant, intron_variant | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.1032+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_033380.3 | ||||
COL4A5 | ENST00000483338.1 | c.-145+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | |||||
COL4A5 | ENST00000361603.7 | c.1032+5G>T | splice_donor_5th_base_variant, intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD4 exome AF: 0.00000230 AC: 2AN: 870157Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 288505
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at