chr10-104143452-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_025145.7(CFAP43):c.4132C>T(p.Arg1378Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,860 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 Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. R1378R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_025145.7 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP43 | NM_025145.7 | c.4132C>T | p.Arg1378Ter | stop_gained | 32/38 | ENST00000357060.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP43 | ENST00000357060.8 | c.4132C>T | p.Arg1378Ter | stop_gained | 32/38 | 1 | NM_025145.7 | P1 | |
CFAP43 | ENST00000434629.5 | c.2128C>T | p.Arg710Ter | stop_gained | 17/23 | 1 | |||
CFAP43 | ENST00000457071.5 | c.679C>T | p.Arg227Ter | stop_gained | 6/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251126Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135714
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727174
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Submissions by phenotype
Spermatogenic failure 19 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 25, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at