rs4293342

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014608.6(CYFIP1):​c.-7+11531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,004 control chromosomes in the GnomAD database, including 21,447 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: 𝑓 0.52 ( 21447 hom., cov: 33)

Consequence

CYFIP1
NM_014608.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0670
Variant links:
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CYFIP1NM_014608.6 linkuse as main transcriptc.-7+11531T>C intron_variant ENST00000617928.5 NP_055423.1 Q7L576-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CYFIP1ENST00000617928.5 linkuse as main transcriptc.-7+11531T>C intron_variant 1 NM_014608.6 ENSP00000481038.1 Q7L576-1

Frequencies

GnomAD3 genomes
AF:
0.523
AC:
79462
AN:
151888
Hom.:
21405
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.639
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.391
Gnomad ASJ
AF:
0.489
Gnomad EAS
AF:
0.394
Gnomad SAS
AF:
0.425
Gnomad FIN
AF:
0.541
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.501
Gnomad OTH
AF:
0.512
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.523
AC:
79553
AN:
152004
Hom.:
21447
Cov.:
33
AF XY:
0.520
AC XY:
38655
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.640
Gnomad4 AMR
AF:
0.390
Gnomad4 ASJ
AF:
0.489
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.424
Gnomad4 FIN
AF:
0.541
Gnomad4 NFE
AF:
0.501
Gnomad4 OTH
AF:
0.512
Alfa
AF:
0.504
Hom.:
13316
Bravo
AF:
0.517
Asia WGS
AF:
0.389
AC:
1355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
4.1
DANN
Benign
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4293342; hg19: chr15-22904312; API