rs150404479
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001378189.1(CFAP57):āc.2588T>Cā(p.Ile863Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0134 in 1,549,630 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0098 ( 13 hom., cov: 32)
Exomes š: 0.014 ( 171 hom. )
Consequence
CFAP57
NM_001378189.1 missense
NM_001378189.1 missense
Scores
8
9
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.09
Genes affected
CFAP57 (HGNC:26485): (cilia and flagella associated protein 57) This protein encoded by this gene belongs to the WD repeat-containing family of proteins, which function in the formation of protein-protein complexes in a variety of biological pathways. This family member is thought to function in craniofacial development, possibly in the fusion of lip and palate. A missense mutation in this gene is associated with Van der Woude syndrome 2. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
EBNA1BP2 (HGNC:15531): (EBNA1 binding protein 2) Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal large subunit biogenesis. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005825013).
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0138 (19304/1397560) while in subpopulation NFE AF= 0.0159 (17183/1078508). AF 95% confidence interval is 0.0157. There are 171 homozygotes in gnomad4_exome. There are 9221 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1486 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP57 | NM_001378189.1 | c.2588T>C | p.Ile863Thr | missense_variant | 16/23 | ENST00000372492.9 | NP_001365118.1 | |
LOC105378685 | XR_007066041.1 | n.377-7486A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP57 | ENST00000372492.9 | c.2588T>C | p.Ile863Thr | missense_variant | 16/23 | 5 | NM_001378189.1 | ENSP00000361570 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00979 AC: 1488AN: 151952Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.00909 AC: 1352AN: 148734Hom.: 13 AF XY: 0.00931 AC XY: 746AN XY: 80100
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GnomAD4 exome AF: 0.0138 AC: 19304AN: 1397560Hom.: 171 Cov.: 31 AF XY: 0.0134 AC XY: 9221AN XY: 689310
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GnomAD4 genome AF: 0.00977 AC: 1486AN: 152070Hom.: 13 Cov.: 32 AF XY: 0.00881 AC XY: 655AN XY: 74324
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.
REVEL
Benign
Sift
Uncertain
D;.
Sift4G
Benign
T;T
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at