rs104886399
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 3P and 5B. PM1PP2BP4BS2
The NM_033380.3(COL4A5):c.3923A>G(p.Gln1308Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,209,134 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_033380.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.3923A>G | p.Gln1308Arg | missense_variant | Exon 44 of 53 | 1 | NM_033380.3 | ENSP00000331902.7 | ||
COL4A5 | ENST00000361603.7 | c.3905A>G | p.Gln1302Arg | missense_variant | Exon 42 of 51 | 2 | ENSP00000354505.2 | |||
COL4A5 | ENST00000489230.1 | n.326A>G | non_coding_transcript_exon_variant | Exon 3 of 8 | 5 | |||||
COL4A5 | ENST00000510690.2 | n.417A>G | non_coding_transcript_exon_variant | Exon 2 of 11 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000535 AC: 6AN: 112080Hom.: 0 Cov.: 24 show subpopulations
GnomAD2 exomes AF: 0.0000383 AC: 7AN: 182905 AF XY: 0.0000593 show subpopulations
GnomAD4 exome AF: 0.0000219 AC: 24AN: 1097054Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 10AN XY: 362700 show subpopulations
GnomAD4 genome AF: 0.0000535 AC: 6AN: 112080Hom.: 0 Cov.: 24 AF XY: 0.0000876 AC XY: 3AN XY: 34238 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
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X-linked Alport syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at