12-121923864-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_144668.6(CFAP251):c.621G>A(p.Glu207=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00045 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000059 ( 0 hom. )
Consequence
CFAP251
NM_144668.6 synonymous
NM_144668.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.39
Genes affected
CFAP251 (HGNC:28506): (cilia and flagella associated protein 251) 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 appears to function in the determination of mean platelet volume (MPV), and polymorphisms in this gene have been associated with variance in MPV. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 12-121923864-G-A is Benign according to our data. Variant chr12-121923864-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3048403.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.39 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP251 | NM_144668.6 | c.621G>A | p.Glu207= | synonymous_variant | 3/22 | ENST00000288912.9 | |
CFAP251 | NM_001178003.2 | c.621G>A | p.Glu207= | synonymous_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP251 | ENST00000288912.9 | c.621G>A | p.Glu207= | synonymous_variant | 3/22 | 1 | NM_144668.6 | ||
CFAP251 | ENST00000397454.2 | c.621G>A | p.Glu207= | synonymous_variant | 3/18 | 1 | P1 | ||
CFAP251 | ENST00000540779.1 | n.519G>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000454 AC: 69AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000922 AC: 23AN: 249516Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135394
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GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727246
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GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74420
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
CFAP251-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2019 | 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
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at