rs10752212

Variant names:

• chr10-10875158-G-A
• rs10752212
• NM_001326325.2:c.110+29002G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

CELF2 Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy 97

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• undetermined early-onset epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001326325.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF2	NM_001326325.2		c.110+29002G>A		intron	N/A	NP_001313254.1
	CELF2	NM_001326327.2		c.54-44806G>A		intron	N/A	NP_001313256.1	A0A1B0GUN8
	CELF2	NM_001326326.2		c.54-44806G>A		intron	N/A	NP_001313255.1	A0A1B0GU44

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF2	ENST00000637215.1	TSL:5	c.54-44806G>A		intron	N/A	ENSP00000490185.1	A0A1B0GUN8
	CELF2	ENST00000636488.1	TSL:5	c.54-44806G>A		intron	N/A	ENSP00000489955.1	A0A1B0GU44
	CELF2	ENST00000638035.1	TSL:5	c.-56+29002G>A		intron	N/A	ENSP00000490401.1	O95319-2

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

African (AFR) AF: 0.871 AC: 36149 AN: 41512

American (AMR) AF: 0.618 AC: 9437 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3468

East Asian (EAS) AF: 0.973 AC: 5030 AN: 5170

South Asian (SAS) AF: 0.665 AC: 3209 AN: 4824

European-Finnish (FIN) AF: 0.584 AC: 6165 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33322 AN: 67934

Other (OTH) AF: 0.596 AC: 1259 AN: 2112

Alfa AF: 0.549 Hom.: 34496

Bravo AF: 0.650

Asia WGS AF: 0.846 AC: 2919 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.9
DANN	Benign	0.64
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10752212; hg19: chr10-10917121;