rs201119

chr10-11008014-T-C

Variant summary

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

The ENST00000416382.6(CELF2):c.53+2574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,096 control chromosomes in the GnomAD database, including 9,997 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 0.26 (9997 hom., cov: 32)
• Consequence: CELF2 ENST00000416382.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

Genes affected

CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) 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. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001025077.3	c.53+2574T>C		intron_variant
CELF2	NM_001326317.2	c.-20+88015T>C		intron_variant
CELF2	NM_001326318.2	c.-20+88015T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2	ENST00000416382.6	c.53+2574T>C		intron_variant		1
CELF2	ENST00000631460.1	c.53+2574T>C		intron_variant		5
CELF2	ENST00000631816.1	c.53+2574T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39539 AN: 151978 Hom.: 9962 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0574

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.260 AC: 39618 AN: 152096 Hom.: 9997 Cov.: 32 AF XY: 0.250 AC XY: 18625 AN XY: 74370

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0575

Gnomad4 FIN AF: 0.0415

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.228

Alfa AF: 0.140 Hom.: 3246

Bravo AF: 0.288

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.9
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs201119; hg19: chr10-11049977;