19-3293595-A-G

Variant names:

• chr19-3293595-A-G
• rs313784
• ENST00000541430.6:c.*261A>G

Variant summary

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

The ENST00000541430.6(CELF5):​c.*261A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 947,640 control chromosomes in the GnomAD database, including 251,455 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 0.74 (41752 hom., cov: 27)
  • Exomes 𝑓: 0.72 (209703 hom.)
• Consequence: CELF5 ENST00000541430.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 8 publications found

Genes affected

CELF5 (HGNC:14058): (CUGBP Elav-like family member 5) This gene encodes a member of the the CELF/BRUNOL protein family, which 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. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF5	NM_021938.4	c.*40+109A>G		intron_variant	Intron 12 of 12	ENST00000292672.7	NP_068757.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF5	ENST00000292672.7	c.*40+109A>G		intron_variant	Intron 12 of 12	1	NM_021938.4	ENSP00000292672.1

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111107 AN: 151082 Hom.: 41700 Cov.: 27

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.717 AC: 571111 AN: 796442 Hom.: 209703 Cov.: 10 AF XY: 0.714 AC XY: 286604 AN XY: 401476

African (AFR) AF: 0.812 AC: 15230 AN: 18762

American (AMR) AF: 0.662 AC: 13361 AN: 20198

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 12495 AN: 15992

East Asian (EAS) AF: 0.245 AC: 7971 AN: 32484

South Asian (SAS) AF: 0.593 AC: 31554 AN: 53202

European-Finnish (FIN) AF: 0.695 AC: 21204 AN: 30512

Middle Eastern (MID) AF: 0.746 AC: 2555 AN: 3424

European-Non Finnish (NFE) AF: 0.752 AC: 439587 AN: 584258

Other (OTH) AF: 0.722 AC: 27154 AN: 37610

GnomAD4 genome AF: 0.736 AC: 111215 AN: 151198 Hom.: 41752 Cov.: 27 AF XY: 0.726 AC XY: 53596 AN XY: 73822

African (AFR) AF: 0.809 AC: 33366 AN: 41234

American (AMR) AF: 0.699 AC: 10610 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2724 AN: 3460

East Asian (EAS) AF: 0.269 AC: 1353 AN: 5028

South Asian (SAS) AF: 0.591 AC: 2830 AN: 4788

European-Finnish (FIN) AF: 0.686 AC: 7139 AN: 10404

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.748 AC: 50730 AN: 67806

Other (OTH) AF: 0.754 AC: 1578 AN: 2094

Alfa AF: 0.738 Hom.: 137680

Bravo AF: 0.738

Asia WGS AF: 0.483 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.028
DANN	Benign	0.30
PhyloP100		-4.1
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: rs313784; hg19: chr19-3293593;