5-157285467-A-G

Variant names:

• chr5-157285467-A-G
• rs1186118351
• NM_001037333.3:c.106A>G

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2 BP4_Moderate BS2

The NM_001037333.3(CYFIP2):​c.106A>G​(p.Ile36Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000777 in 1,416,174 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000078 (0 hom.)
• Consequence: CYFIP2 NM_001037333.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.06

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PP2: Missense variant in the CYFIP2 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 20 curated pathogenic missense variants (we use a threshold of 10). The gene has 46 curated benign missense variants. Gene score misZ: 6.0129 (above the threshold of 3.09). Trascript score misZ: 6.9267 (above the threshold of 3.09). GenCC associations: The gene is linked to developmental and epileptic encephalopathy, 65, developmental and epileptic encephalopathy, 76, undetermined early-onset epileptic encephalopathy.
• BP4: Computational evidence support a benign effect (MetaRNN=0.2342991).
• BS2: High AC in GnomAdExome4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYFIP2	NM_001037333.3	c.106A>G	p.Ile36Val	missense_variant	Exon 2 of 31	ENST00000620254.5	NP_001032410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYFIP2	ENST00000620254.5	c.106A>G	p.Ile36Val	missense_variant	Exon 2 of 31	1	NM_001037333.3	ENSP00000479968.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000777 AC: 11 AN: 1416174 Hom.: 0 Cov.: 30 AF XY: 0.0000100 AC XY: 7 AN XY: 699846

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000919

Gnomad4 OTH exome AF: 0.0000170

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Oct 25, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 36 of the CYFIP2 protein (p.Ile36Val). This variant has not been reported in the literature in individuals affected with CYFIP2-related conditions. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Uncertain	0.98
DEOGEN2	Benign	0.14	T;.;.;T;T;T;.;.;.
Eigen	Benign	-0.079
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.90	D;.;D;D;D;D;D;D;D
M_CAP	Benign	0.0077	T
MetaRNN	Benign	0.23	T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.42	N;N;.;.;.;.;.;.;N
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-0.50	.;.;N;.;N;.;.;.;.
REVEL	Benign	0.10
Sift	Benign	0.56	.;.;T;.;T;.;.;.;.
Sift4G	Benign	0.64	T;T;T;T;T;T;T;T;T
Polyphen		0.063	B;B;B;.;B;.;.;.;B
Vest4		0.21
MutPred		0.38		Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);Gain of phosphorylation at Y38 (P = 0.1011);
MVP		0.37
MPC		0.95
ClinPred		0.65	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.23
gMVP		0.91

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

Other links and lift over

dbSNP: rs1186118351; hg19: chr5-156712477;