10-104380092-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001008723.2(CFAP58):c.1237G>A(p.Ala413Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000392 in 1,614,126 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001008723.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP58 | NM_001008723.2 | c.1237G>A | p.Ala413Thr | missense_variant | 9/18 | ENST00000369704.8 | |
CFAP58 | NM_001400226.1 | c.1183G>A | p.Ala395Thr | missense_variant | 10/19 | ||
CFAP58 | NM_001400227.1 | c.1183G>A | p.Ala395Thr | missense_variant | 9/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP58 | ENST00000369704.8 | c.1237G>A | p.Ala413Thr | missense_variant | 9/18 | 1 | NM_001008723.2 | P1 | |
CFAP58 | ENST00000369703.1 | c.103G>A | p.Ala35Thr | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000480 AC: 73AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000573 AC: 144AN: 251122Hom.: 0 AF XY: 0.000560 AC XY: 76AN XY: 135706
GnomAD4 exome AF: 0.000382 AC: 559AN: 1461842Hom.: 1 Cov.: 31 AF XY: 0.000386 AC XY: 281AN XY: 727218
GnomAD4 genome ? AF: 0.000479 AC: 73AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74452
ClinVar
Submissions by phenotype
CFAP58-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 15, 2023 | The CFAP58 c.1237G>A variant is predicted to result in the amino acid substitution p.Ala413Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.15% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/10-106139850-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at