chrX-108694826-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 4P and 3B. PM1PP3_ModerateBP6_ModerateBS2_Supporting
The NM_033380.3(COL4A5):c.4726C>T(p.Pro1576Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000183 in 1,095,033 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1576A) has been classified as Uncertain significance.
Frequency
Consequence
NM_033380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.4726C>T | p.Pro1576Ser | missense_variant | 51/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.4726C>T | p.Pro1576Ser | missense_variant | 51/53 | 1 | NM_033380.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183041Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67637
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1095033Hom.: 0 Cov.: 28 AF XY: 0.00000555 AC XY: 2AN XY: 360539
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at