rs312926

Positions:

• chr19-3275317-C-T

Variant summary

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

The NM_021938.4(CELF5):​c.395-539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,080 control chromosomes in the GnomAD database, including 19,084 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 0.49 (19084 hom., cov: 32)
• Consequence: CELF5 NM_021938.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF5	NM_021938.4	c.395-539C>T		intron_variant		ENST00000292672.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF5	ENST00000292672.7	c.395-539C>T		intron_variant		1	NM_021938.4	P1

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73866 AN: 151962 Hom.: 19066 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.486 AC: 73952 AN: 152080 Hom.: 19084 Cov.: 32 AF XY: 0.481 AC XY: 35728 AN XY: 74316

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.437

Alfa AF: 0.440 Hom.: 11043

Bravo AF: 0.492

Asia WGS AF: 0.406 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs312926; hg19: chr19-3275315;