rs201082

Positions:

• chr10-10963741-G-A

Variant summary

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

The NM_001326325.2(CELF2):​c.146+43742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,124 control chromosomes in the GnomAD database, including 9,230 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 0.27 (9230 hom., cov: 32)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.973

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]

ENSG00000231496 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326325.2	c.146+43742G>A		intron_variant			NP_001313254.1
CELF2	NM_001326327.2	c.89+43742G>A		intron_variant			NP_001313256.1
CELF2	NM_001326326.2	c.89+43742G>A		intron_variant			NP_001313255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELF2	ENST00000637215.1	c.89+43742G>A		intron_variant		5		ENSP00000490185.1
CELF2	ENST00000636488.1	c.89+43742G>A		intron_variant		5		ENSP00000489955.1
CELF2	ENST00000638035.1	c.-20+43742G>A		intron_variant		5		ENSP00000490401.1
ENSG00000231496	ENST00000420825.2	n.217-2821G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41767 AN: 152006 Hom.: 9204 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0956

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.275 AC: 41832 AN: 152124 Hom.: 9230 Cov.: 32 AF XY: 0.264 AC XY: 19664 AN XY: 74376

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0959

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.242

Alfa AF: 0.182 Hom.: 1729

Bravo AF: 0.300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201082; hg19: chr10-11005704;