rs10752212

chr10-10875158-G-A

Variant summary

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

The NM_001326325.2(CELF2):c.110+29002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,050 control chromosomes in the GnomAD database, including 33,132 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 0.64 (33132 hom., cov: 33)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-55-44806G>A		intron_variant
CELF2	NM_001326318.2	c.-55-44806G>A		intron_variant
CELF2	NM_001326319.2	c.-93-44806G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2	ENST00000636488.1	c.54-44806G>A		intron_variant		5
CELF2	ENST00000637215.1	c.54-44806G>A		intron_variant		5
CELF2	ENST00000638035.1	c.-56+29002G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96662 AN: 151932 Hom.: 33063 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.637 AC: 96790 AN: 152050 Hom.: 33132 Cov.: 33 AF XY: 0.643 AC XY: 47763 AN XY: 74286

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.596

Alfa AF: 0.606 Hom.: 5314

Bravo AF: 0.650

Asia WGS AF: 0.846 AC: 2919 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	3.9
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10752212; hg19: chr10-10917121;