15-22874595-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_014608.6(CYFIP1):c.3165C>T(p.Ala1055=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000983 in 1,607,000 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 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000093 ( 0 hom. )
Consequence
CYFIP1
NM_014608.6 synonymous
NM_014608.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.372
Genes affected
CYFIP1 (HGNC:13759): (cytoplasmic FMR1 interacting protein 1) This gene encodes a protein that regulates cytoskeletal dynamics and protein translation. The encoded protein is a component of the WAVE regulatory complex (WRC), which promotes actin polymerization. This protein also interacts with the synaptic functional regulator FMR1 protein and translation initiation factor 4E to inhibit protein translation. A large chromosomal deletion including this gene is associated with increased risk of schizophrenia and epilepsy in human patients. Reduced expression of this gene has been observed in various human cancers and the encoded protein may inhibit tumor invasion. [provided by RefSeq, Mar 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 15-22874595-G-A is Benign according to our data. Variant chr15-22874595-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 744883.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.372 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYFIP1 | NM_014608.6 | c.3165C>T | p.Ala1055= | synonymous_variant | 28/31 | ENST00000617928.5 | NP_055423.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYFIP1 | ENST00000617928.5 | c.3165C>T | p.Ala1055= | synonymous_variant | 28/31 | 1 | NM_014608.6 | ENSP00000481038 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152186Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000161 AC: 39AN: 242564Hom.: 0 AF XY: 0.000182 AC XY: 24AN XY: 131582
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GnomAD4 exome AF: 0.0000928 AC: 135AN: 1454696Hom.: 0 Cov.: 30 AF XY: 0.000112 AC XY: 81AN XY: 723700
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GnomAD4 genome AF: 0.000151 AC: 23AN: 152304Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 12, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at