chr1-207113083-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000715.4(C4BPA):c.58T>C(p.Trp20Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,610,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000715.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4BPA | NM_000715.4 | c.58T>C | p.Trp20Arg | missense_variant | 2/12 | ENST00000367070.8 | |
C4BPA | XM_005273251.3 | c.58T>C | p.Trp20Arg | missense_variant | 2/12 | ||
C4BPA | XM_005273252.5 | c.58T>C | p.Trp20Arg | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4BPA | ENST00000367070.8 | c.58T>C | p.Trp20Arg | missense_variant | 2/12 | 1 | NM_000715.4 | P1 | |
C4BPA | ENST00000421786.5 | c.58T>C | p.Trp20Arg | missense_variant | 2/5 | 4 | |||
C4BPA | ENST00000424088.1 | c.58T>C | p.Trp20Arg | missense_variant, NMD_transcript_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246558Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133348
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458526Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 725478
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.58T>C (p.W20R) alteration is located in exon 2 (coding exon 1) of the C4BPA gene. This alteration results from a T to C substitution at nucleotide position 58, causing the tryptophan (W) at amino acid position 20 to be replaced by an arginine (R). 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