rs7099713

Positions:

• chr10-11011180-A-C

Variant summary

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

The ENST00000416382.6(CELF2):​c.53+5740A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,220 control chromosomes in the GnomAD database, including 354 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 0.066 (354 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CELF2 ENST00000416382.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

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]

LOC124902376 (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 (AFR) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902376	XR_007062052.1	n.77T>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2	ENST00000416382.6	c.53+5740A>C		intron_variant		1
CELF2	ENST00000631460.1	c.53+5740A>C		intron_variant		5
CELF2	ENST00000631816.1	c.53+5740A>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9972 AN: 152102 Hom.: 353 Cov.: 31

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0751

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0656 AC: 9980 AN: 152220 Hom.: 354 Cov.: 31 AF XY: 0.0623 AC XY: 4638 AN XY: 74426

Gnomad4 AFR AF: 0.0795

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0679 Hom.: 235

Bravo AF: 0.0705

Asia WGS AF: 0.0130 AC: 44 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	8.7
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7099713; hg19: chr10-11053143;