rs650680

chr18-37382905-G-A

Variant summary

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

The NM_020180.4(CELF4):c.370-61024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,876 control chromosomes in the GnomAD database, including 18,078 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 0.48 (18078 hom., cov: 31)
• Consequence: CELF4 NM_020180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF4	NM_020180.4	c.370-61024C>T		intron_variant		ENST00000420428.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF4	ENST00000420428.7	c.370-61024C>T		intron_variant		5	NM_020180.4	P4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72864 AN: 151758 Hom.: 18050 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.480 AC: 72946 AN: 151876 Hom.: 18078 Cov.: 31 AF XY: 0.479 AC XY: 35574 AN XY: 74226

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.700

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.491

Alfa AF: 0.453 Hom.: 1970

Bravo AF: 0.494

Asia WGS AF: 0.590 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.0
Dann	Benign	0.78

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: rs650680; hg19: chr18-34962868;