15-22923240-T-C

Variant names:

• chr15-22923240-T-C
• rs1579821
• NM_014608.6:c.1359+2742A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014608.6(CYFIP1):​c.1359+2742A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,990 control chromosomes in the GnomAD database, including 4,720 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 0.25 (4720 hom., cov: 32)
• Consequence: CYFIP1 NM_014608.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014608.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYFIP1	NM_014608.6	MANE Select	c.1359+2742A>G		intron	N/A	NP_055423.1
	CYFIP1	NM_001324119.2		c.1461+2742A>G		intron	N/A	NP_001311048.1
	CYFIP1	NM_001287810.4		c.1359+2742A>G		intron	N/A	NP_001274739.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYFIP1	ENST00000617928.5	TSL:1 MANE Select	c.1359+2742A>G		intron	N/A	ENSP00000481038.1
	CYFIP1	ENST00000610365.4	TSL:1	c.1359+2742A>G		intron	N/A	ENSP00000478779.1
	CYFIP1	ENST00000612288.2	TSL:3	c.1359+2742A>G		intron	N/A	ENSP00000479802.2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37289 AN: 151872 Hom.: 4708 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.233

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.246 AC: 37320 AN: 151990 Hom.: 4720 Cov.: 32 AF XY: 0.242 AC XY: 18009 AN XY: 74280

African (AFR) AF: 0.212 AC: 8792 AN: 41456

American (AMR) AF: 0.194 AC: 2968 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1225 AN: 5176

South Asian (SAS) AF: 0.239 AC: 1151 AN: 4810

European-Finnish (FIN) AF: 0.248 AC: 2615 AN: 10558

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18712 AN: 67944

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.262 Hom.: 8974

Bravo AF: 0.235

Asia WGS AF: 0.273 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		0.45

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

Other links and lift over

dbSNP: rs1579821; hg19: chr15-22949828;