rs992193

Variant names:

• chr10-10931353-C-T
• rs992193
• NM_001326325.2:c.146+11354C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001326325.2(CELF2):​c.146+11354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,832 control chromosomes in the GnomAD database, including 30,740 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 0.63 (30740 hom., cov: 30)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

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]

LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001326325.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF2	NM_001326325.2		c.146+11354C>T		intron	N/A	NP_001313254.1
	CELF2	NM_001326327.2		c.89+11354C>T		intron	N/A	NP_001313256.1	A0A1B0GUN8
	CELF2	NM_001326326.2		c.89+11354C>T		intron	N/A	NP_001313255.1	A0A1B0GU44

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF2	ENST00000637215.1	TSL:5	c.89+11354C>T		intron	N/A	ENSP00000490185.1	A0A1B0GUN8
	CELF2	ENST00000636488.1	TSL:5	c.89+11354C>T		intron	N/A	ENSP00000489955.1	A0A1B0GU44
	CELF2	ENST00000638035.1	TSL:5	c.-20+11354C>T		intron	N/A	ENSP00000490401.1	O95319-2

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95878 AN: 151714 Hom.: 30740 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.632 AC: 95900 AN: 151832 Hom.: 30740 Cov.: 30 AF XY: 0.632 AC XY: 46904 AN XY: 74172

African (AFR) AF: 0.547 AC: 22612 AN: 41370

American (AMR) AF: 0.570 AC: 8691 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2523 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2658 AN: 5146

South Asian (SAS) AF: 0.757 AC: 3623 AN: 4786

European-Finnish (FIN) AF: 0.683 AC: 7196 AN: 10536

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46583 AN: 67954

Other (OTH) AF: 0.638 AC: 1346 AN: 2110

Alfa AF: 0.664 Hom.: 61863

Bravo AF: 0.615

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.52
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs992193; hg19: chr10-10973316;