rs4799934

chr18-37523704-A-Cchr18-37523704-A-Gchr18-37523704-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020180.4(CELF4):c.287-38097T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,258 control chromosomes in the GnomAD database, including 60,792 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 0.89 (60792 hom., cov: 34)
• Consequence: CELF4 NM_020180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

CELF4 (HGNC:14015): (CUGBP Elav-like family member 4) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF4	NM_020180.4	c.287-38097T>G		intron_variant		ENST00000420428.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF4	ENST00000420428.7	c.287-38097T>G		intron_variant		5	NM_020180.4	P4

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135461 AN: 152140 Hom.: 60757 Cov.: 34

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.890 AC: 135547 AN: 152258 Hom.: 60792 Cov.: 34 AF XY: 0.892 AC XY: 66388 AN XY: 74458

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.913

Alfa AF: 0.922 Hom.: 58724

Bravo AF: 0.871

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.2
Dann	Benign	0.46

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: rs4799934; hg19: chr18-35103667;