rs1422638161
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3PP5_Moderate
The NM_000091.5(COL4A3):c.890G>A(p.Gly297Glu) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000274 in 1,461,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_000091.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A3 | NM_000091.5 | c.890G>A | p.Gly297Glu | missense_variant, splice_region_variant | 16/52 | ENST00000396578.8 | |
MFF-DT | NR_102371.1 | n.1592+3151C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A3 | ENST00000396578.8 | c.890G>A | p.Gly297Glu | missense_variant, splice_region_variant | 16/52 | 1 | NM_000091.5 | P1 | |
MFF-DT | ENST00000439598.6 | n.1592+3151C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249382Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135304
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461568Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727088
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Autosomal recessive Alport syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Nov 13, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at