2-227238016-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP3BP4BP6
The NM_000091.5(COL4A3):c.136G>A(p.Gly46Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000102 in 1,605,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000091.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000598 AC: 91AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000164 AC: 41AN: 249530Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135380
GnomAD4 exome AF: 0.0000496 AC: 72AN: 1452848Hom.: 0 Cov.: 27 AF XY: 0.0000498 AC XY: 36AN XY: 723394
GnomAD4 genome AF: 0.000598 AC: 91AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:2
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Inborn genetic diseases Uncertain:1
The c.136G>A (p.G46R) alteration is located in exon 2 (coding exon 2) of the COL4A3 gene. This alteration results from a G to A substitution at nucleotide position 136, causing the glycine (G) at amino acid position 46 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Autosomal dominant Alport syndrome Uncertain:1
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COL4A3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at