rs10508421

chr10-11321772-T-C

Variant summary

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

The NM_001326342.2(CELF2):c.1294+386T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,296 control chromosomes in the GnomAD database, including 602 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 0.077 (602 hom., cov: 32)
• Consequence: CELF2 NM_001326342.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326342.2	c.1294+386T>C		intron_variant		ENST00000633077.2
CELF2-AS1	NR_126062.1	n.195+1798A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2	ENST00000633077.2	c.1294+386T>C		intron_variant		1	NM_001326342.2	P1

Frequencies

GnomAD3 genomes AF: 0.0774 AC: 11785 AN: 152178 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0773 AC: 11774 AN: 152296 Hom.: 602 Cov.: 32 AF XY: 0.0782 AC XY: 5826 AN XY: 74462

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.105 Hom.: 407

Bravo AF: 0.0701

Asia WGS AF: 0.0430 AC: 150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.61
Dann	Benign	0.57

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: rs10508421; hg19: chr10-11363735;