chr11-47478715-T-C

Variant names:

• chr11-47478715-T-C
• rs2242081
• NM_001376376.1:c.844+162A>G

Variant summary

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

The ENST00000687097.1(CELF1):​c.844+162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,080 control chromosomes in the GnomAD database, including 10,462 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 (10462 hom., cov: 32)
• Consequence: CELF1 ENST00000687097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 31 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687097.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF1	NM_001376376.1	MANE Select	c.844+162A>G		intron	N/A	NP_001363305.1
	CELF1	NM_001330272.2		c.844+162A>G		intron	N/A	NP_001317201.1
	CELF1	NM_001376369.1		c.844+162A>G		intron	N/A	NP_001363298.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CELF1	ENST00000687097.1	MANE Select	c.844+162A>G		intron	N/A	ENSP00000508525.1
	CELF1	ENST00000532048.5	TSL:1	c.841+162A>G		intron	N/A	ENSP00000435926.1
	CELF1	ENST00000358597.7	TSL:1	c.763+162A>G		intron	N/A	ENSP00000351409.3

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53135 AN: 151962 Hom.: 10463 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.349 AC: 53132 AN: 152080 Hom.: 10462 Cov.: 32 AF XY: 0.346 AC XY: 25722 AN XY: 74322

African (AFR) AF: 0.174 AC: 7223 AN: 41498

American (AMR) AF: 0.321 AC: 4899 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.391 AC: 2023 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4822

European-Finnish (FIN) AF: 0.345 AC: 3647 AN: 10570

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30035 AN: 67960

Other (OTH) AF: 0.394 AC: 829 AN: 2106

Alfa AF: 0.419 Hom.: 25801

Bravo AF: 0.336

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.50
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2242081; hg19: chr11-47500267;