NM_001376376.1:c.-153-9400A>C

Variant names:

• chr11-47510332-T-G
• rs4752843
• NM_001376376.1:c.-153-9400A>C

Variant summary

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

The NM_001376376.1(CELF1):​c.-153-9400A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,056 control chromosomes in the GnomAD database, including 3,708 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 0.20 (3708 hom., cov: 31)
• Consequence: CELF1 NM_001376376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF1	NM_001376376.1	c.-153-9400A>C		intron_variant	Intron 1 of 14	ENST00000687097.1	NP_001363305.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF1	ENST00000687097.1	c.-153-9400A>C		intron_variant	Intron 1 of 14		NM_001376376.1	ENSP00000508525.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31147 AN: 151938 Hom.: 3711 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.205 AC: 31154 AN: 152056 Hom.: 3708 Cov.: 31 AF XY: 0.212 AC XY: 15759 AN XY: 74334

African (AFR) AF: 0.294 AC: 12180 AN: 41442

American (AMR) AF: 0.220 AC: 3371 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3460

East Asian (EAS) AF: 0.303 AC: 1564 AN: 5170

South Asian (SAS) AF: 0.162 AC: 780 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10574

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9491 AN: 67986

Other (OTH) AF: 0.165 AC: 348 AN: 2108

Alfa AF: 0.143 Hom.: 726

Bravo AF: 0.207

Asia WGS AF: 0.198 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4752843; hg19: chr11-47531884;