rs9329334

chr10-11327907-C-T

Variant summary

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

The NM_001326342.2(CELF2):c.1439-1019C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,034 control chromosomes in the GnomAD database, including 5,653 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 (5653 hom., cov: 32)
• Consequence: CELF2 NM_001326342.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326342.2	c.1439-1019C>T		intron_variant		ENST00000633077.2
CELF2-AS1	NR_126062.1	n.98-4240G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2	ENST00000633077.2	c.1439-1019C>T		intron_variant		1	NM_001326342.2	P1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39764 AN: 151916 Hom.: 5657 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.262 AC: 39759 AN: 152034 Hom.: 5653 Cov.: 32 AF XY: 0.261 AC XY: 19431 AN XY: 74322

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.303

Alfa AF: 0.297 Hom.: 6308

Bravo AF: 0.271

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.4
Dann	Benign	0.69

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: rs9329334; hg19: chr10-11369870;