chrX-108626251-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_033380.3(COL4A5):c.3148C>T(p.Pro1050Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000238 in 1,208,151 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 82 hemizygotes in GnomAD. In-silico tool predicts a benign 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. P1050A) has been classified as Uncertain significance.
Frequency
Consequence
NM_033380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.3148C>T | p.Pro1050Ser | missense_variant | 36/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.3148C>T | p.Pro1050Ser | missense_variant | 36/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000483338.1 | c.1972C>T | p.Pro658Ser | missense_variant | 20/20 | 1 | |||
COL4A5 | ENST00000361603.7 | c.3148C>T | p.Pro1050Ser | missense_variant | 36/51 | 2 | P1 | ||
COL4A5 | ENST00000505728.1 | c.382C>T | p.Pro128Ser | missense_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00138 AC: 154AN: 111348Hom.: 0 Cov.: 22 AF XY: 0.00131 AC XY: 44AN XY: 33530
GnomAD3 exomes AF: 0.000377 AC: 69AN: 183192Hom.: 0 AF XY: 0.000310 AC XY: 21AN XY: 67732
GnomAD4 exome AF: 0.000122 AC: 134AN: 1096751Hom.: 0 Cov.: 29 AF XY: 0.000105 AC XY: 38AN XY: 362365
GnomAD4 genome AF: 0.00138 AC: 154AN: 111400Hom.: 0 Cov.: 22 AF XY: 0.00131 AC XY: 44AN XY: 33592
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 10, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 28, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 19, 2017 | - - |
COL4A5-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 05, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
X-linked Alport syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 29, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at