chr10-104380050-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001008723.2(CFAP58):c.1195G>A(p.Ala399Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A399V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001008723.2 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 |
---|---|---|---|---|---|---|---|
CFAP58 | NM_001008723.2 | c.1195G>A | p.Ala399Thr | missense_variant | 9/18 | ENST00000369704.8 | |
CFAP58 | NM_001400226.1 | c.1141G>A | p.Ala381Thr | missense_variant | 10/19 | ||
CFAP58 | NM_001400227.1 | c.1141G>A | p.Ala381Thr | missense_variant | 9/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP58 | ENST00000369704.8 | c.1195G>A | p.Ala399Thr | missense_variant | 9/18 | 1 | NM_001008723.2 | P1 | |
CFAP58 | ENST00000369703.1 | c.61G>A | p.Ala21Thr | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250812Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135538
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461706Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727156
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.1195G>A (p.A399T) alteration is located in exon 9 (coding exon 9) of the CFAP58 gene. This alteration results from a G to A substitution at nucleotide position 1195, causing the alanine (A) at amino acid position 399 to be replaced by a threonine (T). 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