rs10905868

Variant names:

• chr10-10932293-A-G
• rs10905868
• NM_001326325.2:c.146+12294A>G

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+12294A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,994 control chromosomes in the GnomAD database, including 4,404 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 0.24 (4404 hom., cov: 31)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF2	NM_001326325.2	c.146+12294A>G		intron_variant	Intron 3 of 15		NP_001313254.1
CELF2	NM_001326327.2	c.89+12294A>G		intron_variant	Intron 2 of 14		NP_001313256.1
CELF2	NM_001326326.2	c.89+12294A>G		intron_variant	Intron 2 of 14		NP_001313255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF2	ENST00000637215.1	c.89+12294A>G		intron_variant	Intron 2 of 14	5		ENSP00000490185.1
CELF2	ENST00000636488.1	c.89+12294A>G		intron_variant	Intron 2 of 13	5		ENSP00000489955.1
CELF2	ENST00000638035.1	c.-20+12294A>G		intron_variant	Intron 3 of 14	5		ENSP00000490401.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35901 AN: 151876 Hom.: 4396 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.236 AC: 35933 AN: 151994 Hom.: 4404 Cov.: 31 AF XY: 0.236 AC XY: 17530 AN XY: 74302

African (AFR) AF: 0.275 AC: 11411 AN: 41440

American (AMR) AF: 0.184 AC: 2814 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 582 AN: 3470

East Asian (EAS) AF: 0.155 AC: 802 AN: 5162

South Asian (SAS) AF: 0.269 AC: 1292 AN: 4808

European-Finnish (FIN) AF: 0.241 AC: 2551 AN: 10564

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15871 AN: 67960

Other (OTH) AF: 0.210 AC: 443 AN: 2112

Alfa AF: 0.230 Hom.: 11114

Bravo AF: 0.231

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10905868; hg19: chr10-10974256;