chr21-44330206-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM1BP4_StrongBP6BS1BS2
The NM_004928.3(CFAP410):c.763G>A(p.Ala255Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,568,058 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004928.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP410 | NM_004928.3 | c.763G>A | p.Ala255Thr | missense_variant | Exon 7 of 7 | ENST00000339818.9 | NP_004919.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000663 AC: 101AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000641 AC: 113AN: 176270Hom.: 1 AF XY: 0.000603 AC XY: 58AN XY: 96124
GnomAD4 exome AF: 0.00143 AC: 2030AN: 1415690Hom.: 3 Cov.: 30 AF XY: 0.00139 AC XY: 975AN XY: 701162
GnomAD4 genome AF: 0.000663 AC: 101AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74510
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2025 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2017 | - - |
CFAP410-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 05, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at