19-13799870-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001367834.3(ZSWIM4):c.304C>T(p.Arg102Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000707 in 1,613,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367834.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZSWIM4 | NM_001367834.3 | c.304C>T | p.Arg102Cys | missense_variant | Exon 2 of 14 | ENST00000590508.6 | NP_001354763.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZSWIM4 | ENST00000590508.6 | c.304C>T | p.Arg102Cys | missense_variant | Exon 2 of 14 | 2 | NM_001367834.3 | ENSP00000468285.2 | ||
ZSWIM4 | ENST00000254323.6 | c.304C>T | p.Arg102Cys | missense_variant | Exon 2 of 13 | 2 | ENSP00000254323.2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 249806Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135544
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461116Hom.: 0 Cov.: 32 AF XY: 0.0000812 AC XY: 59AN XY: 726880
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.304C>T (p.R102C) alteration is located in exon 2 (coding exon 2) of the ZSWIM4 gene. This alteration results from a C to T substitution at nucleotide position 304, causing the arginine (R) at amino acid position 102 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at