chr18-37325148-C-T

Position:

• chr18-37325148-C-T

Variant summary

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

The NM_020180.4(CELF4):​c.370-3267G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,666 control chromosomes in the GnomAD database, including 18,804 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 0.49 (18804 hom., cov: 31)
• Consequence: CELF4 NM_020180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.50

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]

CELF4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF4	NM_020180.4	c.370-3267G>A		intron_variant		ENST00000420428.7	NP_064565.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELF4	ENST00000420428.7	c.370-3267G>A		intron_variant		5	NM_020180.4	ENSP00000410584.2
CELF4	ENST00000603232.6	c.370-3267G>A		intron_variant		1		ENSP00000474788.2
CELF4	ENST00000361795.9	c.370-3267G>A		intron_variant		2		ENSP00000355089.4

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74901 AN: 151550 Hom.: 18799 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.494 AC: 74935 AN: 151666 Hom.: 18804 Cov.: 31 AF XY: 0.503 AC XY: 37249 AN XY: 74118

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.493

Alfa AF: 0.484 Hom.: 9452

Bravo AF: 0.489

Asia WGS AF: 0.722 AC: 2510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.48

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: rs608489; hg19: chr18-34905111;