rs884623

Variant summary

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

The NM_001037333.3(CYFIP2):​c.3040-504G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,106 control chromosomes in the GnomAD database, including 903 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 0.10 ( 903 hom., cov: 32)

Consequence

CYFIP2
NM_001037333.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.199
Variant links:
Genes affected
CYFIP2 (HGNC:13760): (cytoplasmic FMR1 interacting protein 2) Predicted to enable small GTPase binding activity. Involved in activation of cysteine-type endopeptidase activity; apoptotic process; and cell-cell adhesion. Located in perinuclear region of cytoplasm and synapse. Part of SCAR complex. Implicated in developmental and epileptic encephalopathy 65. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CYFIP2NM_001037333.3 linkuse as main transcriptc.3040-504G>A intron_variant ENST00000620254.5
NIPAL4-DTNR_136205.1 linkuse as main transcriptn.94-17481C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CYFIP2ENST00000620254.5 linkuse as main transcriptc.3040-504G>A intron_variant 1 NM_001037333.3 P1Q96F07-2
ENST00000508443.1 linkuse as main transcriptn.727+2127C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.101
AC:
15364
AN:
151988
Hom.:
897
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.154
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.0683
Gnomad ASJ
AF:
0.179
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0602
Gnomad FIN
AF:
0.0477
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.0905
Gnomad OTH
AF:
0.0923
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15388
AN:
152106
Hom.:
903
Cov.:
32
AF XY:
0.0976
AC XY:
7255
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.155
Gnomad4 AMR
AF:
0.0682
Gnomad4 ASJ
AF:
0.179
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0609
Gnomad4 FIN
AF:
0.0477
Gnomad4 NFE
AF:
0.0905
Gnomad4 OTH
AF:
0.0914
Alfa
AF:
0.0976
Hom.:
952
Bravo
AF:
0.107
Asia WGS
AF:
0.0400
AC:
140
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.2
DANN
Benign
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

LitVar

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

Other links and lift over

dbSNP: rs884623; hg19: chr5-156809094; COSMIC: COSV59032679; COSMIC: COSV59032679; API