10-11039984-C-T

Variant names:

• chr10-11039984-C-T
• rs932918
• NM_001326342.2:c.74+21821C>T

Variant summary

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

The NM_001326342.2(CELF2):​c.74+21821C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,978 control chromosomes in the GnomAD database, including 11,000 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 0.34 (11000 hom., cov: 32)
• Consequence: CELF2 NM_001326342.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF2	NM_001326342.2	c.74+21821C>T		intron_variant	Intron 1 of 12	ENST00000633077.2	NP_001313271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF2	ENST00000633077.2	c.74+21821C>T		intron_variant	Intron 1 of 12	1	NM_001326342.2	ENSP00000488690.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51486 AN: 151862 Hom.: 10997 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.339 AC: 51538 AN: 151978 Hom.: 11000 Cov.: 32 AF XY: 0.348 AC XY: 25820 AN XY: 74262

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.307

Alfa AF: 0.224 Hom.: 6438

Bravo AF: 0.351

Asia WGS AF: 0.544 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.37

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: rs932918; hg19: chr10-11081947;