10-10980483-T-C

Position:

• chr10-10980483-T-C

Variant summary

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

The NM_001326325.2(CELF2):​c.146+60484T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,296 control chromosomes in the GnomAD database, including 65,568 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 0.93 (65568 hom., cov: 32)
• Consequence: CELF2 NM_001326325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-20+60484T>C		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-20+60484T>C		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-20+40029T>C		intron_variant			NP_001313248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELF2	ENST00000636488.1	c.89+60484T>C		intron_variant		5		ENSP00000489955
CELF2	ENST00000637215.1	c.89+60484T>C		intron_variant		5		ENSP00000490185
CELF2	ENST00000638035.1	c.-20+60484T>C		intron_variant		5		ENSP00000490401

Frequencies

GnomAD3 genomes AF: 0.927 AC: 141031 AN: 152178 Hom.: 65506 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.927 AC: 141152 AN: 152296 Hom.: 65568 Cov.: 32 AF XY: 0.928 AC XY: 69105 AN XY: 74468

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.944

Alfa AF: 0.900 Hom.: 76514

Bravo AF: 0.936

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201097; hg19: chr10-11022446;