rs7124681

Positions:

• chr11-47508395-C-A
• chr11-47508395-C-T

Variant summary

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

The NM_001376376.1(CELF1):​c.-153-7463G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,560 control chromosomes in the GnomAD database, including 10,356 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 0.36 (10356 hom., cov: 30)
• Consequence: CELF1 NM_001376376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

CELF1 (HGNC:2549): (CUGBP Elav-like family member 1) 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. This gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF1	NM_001376376.1	c.-153-7463G>T		intron_variant		ENST00000687097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF1	ENST00000687097.1	c.-153-7463G>T		intron_variant			NM_001376376.1	P3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55120 AN: 151442 Hom.: 10342 Cov.: 30

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.364 AC: 55165 AN: 151560 Hom.: 10356 Cov.: 30 AF XY: 0.364 AC XY: 26920 AN XY: 74010

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.381

Alfa AF: 0.404 Hom.: 25802

Bravo AF: 0.363

Asia WGS AF: 0.313 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.58
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7124681; hg19: chr11-47529947;