GeneBe

NM_014608.6:c.1527-120T>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014608.6(CYFIP1):​c.1527-120T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000986 in 1,014,072 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 9.9e-7 ( 0 hom. )

Consequence

CYFIP1
NM_014608.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.402

Publications

6 publications found
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 was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYFIP1NM_014608.6 linkc.1527-120T>A intron_variant Intron 14 of 30 ENST00000617928.5 NP_055423.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYFIP1ENST00000617928.5 linkc.1527-120T>A intron_variant Intron 14 of 30 1 NM_014608.6 ENSP00000481038.1
CYFIP1ENST00000610365.4 linkc.1527-120T>A intron_variant Intron 15 of 31 1 ENSP00000478779.1
CYFIP1ENST00000612288.2 linkc.1527-120T>A intron_variant Intron 13 of 29 3 ENSP00000479802.2
CYFIP1ENST00000622576.1 linkn.-148T>A upstream_gene_variant 4 ENSP00000482459.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
9.86e-7
AC:
1
AN:
1014072
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
509132
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22210
American (AMR)
AF:
0.00
AC:
0
AN:
26254
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
17426
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34672
South Asian (SAS)
AF:
0.00
AC:
0
AN:
62906
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46256
Middle Eastern (MID)
AF:
0.000224
AC:
1
AN:
4466
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
755486
Other (OTH)
AF:
0.00
AC:
0
AN:
44396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.85
DANN
Benign
0.16
PhyloP100
-0.40

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

Other links and lift over

dbSNP: rs2289816; hg19: chr15-22955013; API