18-50251567-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145020.5(CFAP53):c.691C>T(p.Arg231Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0297 in 1,614,156 control chromosomes in the GnomAD database, including 7,342 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_145020.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0410 AC: 6239AN: 152170Hom.: 863 Cov.: 33
GnomAD3 exomes AF: 0.0835 AC: 20839AN: 249570Hom.: 3319 AF XY: 0.0726 AC XY: 9835AN XY: 135406
GnomAD4 exome AF: 0.0285 AC: 41629AN: 1461868Hom.: 6473 Cov.: 33 AF XY: 0.0280 AC XY: 20361AN XY: 727238
GnomAD4 genome AF: 0.0411 AC: 6255AN: 152288Hom.: 869 Cov.: 33 AF XY: 0.0478 AC XY: 3562AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Heterotaxy, visceral, 6, autosomal Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at