10-10940683-C-T

Position:

• chr10-10940683-C-T

Variant summary

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

The NM_001326325.2(CELF2):​c.146+20684C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,978 control chromosomes in the GnomAD database, including 10,042 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 0.35 (10042 hom., cov: 32)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

Genes affected

LINC00710 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326325.2	c.146+20684C>T		intron_variant			NP_001313254.1
CELF2	NM_001326327.2	c.89+20684C>T		intron_variant			NP_001313256.1
CELF2	NM_001326326.2	c.89+20684C>T		intron_variant			NP_001313255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00710	ENST00000428520.7	n.687+3500G>A		intron_variant		1
LINC00710	ENST00000635670.2	n.455+3500G>A		intron_variant		1
CELF2	ENST00000637215.1	c.89+20684C>T		intron_variant		5		ENSP00000490185.1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52577 AN: 151862 Hom.: 10030 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.346 AC: 52628 AN: 151978 Hom.: 10042 Cov.: 32 AF XY: 0.359 AC XY: 26681 AN XY: 74296

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.375

Alfa AF: 0.327 Hom.: 4567

Bravo AF: 0.347

Asia WGS AF: 0.591 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10795839; hg19: chr10-10982646;