chr1-196779209-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021023.6(CFHR3):c.106G>T(p.Glu36*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000215 in 1,393,010 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_021023.6 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFHR3 | ENST00000367425.9 | c.106G>T | p.Glu36* | stop_gained | Exon 2 of 6 | 1 | NM_021023.6 | ENSP00000356395.5 | ||
ENSG00000289697 | ENST00000696032.1 | c.3628G>T | p.Glu1210* | stop_gained | Exon 23 of 27 | ENSP00000512341.1 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238176Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 128418
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1393010Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 691760
GnomAD4 genome Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: CFHR3 c.106G>T (p.Glu36X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay. Other truncations within this gene have been classified as variants of uncertain significance internally and in ClinVar. The variant allele was found at a frequency of 4.2e-06 in 238176 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.106G>T in individuals affected with Genetic Atypical Hemolytic Uremic Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at