rs920791
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_145020.5(CFAP53):c.778-12A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,607,288 control chromosomes in the GnomAD database, including 78,808 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 7799 hom., cov: 33)
Exomes 𝑓: 0.31 ( 71009 hom. )
Consequence
CFAP53
NM_145020.5 splice_polypyrimidine_tract, intron
NM_145020.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00002591
2
Clinical Significance
Conservation
PhyloP100: -2.24
Genes affected
CFAP53 (HGNC:26530): (cilia and flagella associated protein 53) This gene belongs to the CFAP53 family. It was found to be differentially expressed by the ciliated cells of frog epidermis and in skin fibroblasts from human. Mutations in this gene are associated with visceral heterotaxy-6, which implicates this gene in determination of left-right asymmetric patterning. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 18-50250988-T-A is Benign according to our data. Variant chr18-50250988-T-A is described in ClinVar as [Benign]. Clinvar id is 262557.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP53 | NM_145020.5 | c.778-12A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000398545.5 | NP_659457.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP53 | ENST00000398545.5 | c.778-12A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_145020.5 | ENSP00000381553 | P1 |
Frequencies
GnomAD3 genomes AF: 0.317 AC: 48215AN: 151998Hom.: 7785 Cov.: 33
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GnomAD3 exomes AF: 0.293 AC: 72999AN: 249256Hom.: 11031 AF XY: 0.295 AC XY: 39837AN XY: 135252
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GnomAD4 exome AF: 0.310 AC: 451598AN: 1455172Hom.: 71009 Cov.: 30 AF XY: 0.310 AC XY: 224600AN XY: 724426
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GnomAD4 genome AF: 0.317 AC: 48264AN: 152116Hom.: 7799 Cov.: 33 AF XY: 0.315 AC XY: 23451AN XY: 74366
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 26, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Heterotaxy, visceral, 6, autosomal Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at