19-3273190-T-C

Variant names:

• chr19-3273190-T-C
• rs312929
• NM_021938.4:c.343-682T>C

Variant summary

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

The NM_021938.4(CELF5):​c.343-682T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,834 control chromosomes in the GnomAD database, including 17,291 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 0.45 (17291 hom., cov: 30)
• Consequence: CELF5 NM_021938.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.536
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF5	NM_021938.4	c.343-682T>C		intron_variant	Intron 2 of 12	ENST00000292672.7	NP_068757.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF5	ENST00000292672.7	c.343-682T>C		intron_variant	Intron 2 of 12	1	NM_021938.4	ENSP00000292672.1

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68963 AN: 151716 Hom.: 17272 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.455 AC: 69032 AN: 151834 Hom.: 17291 Cov.: 30 AF XY: 0.451 AC XY: 33433 AN XY: 74204

African (AFR) AF: 0.686 AC: 28375 AN: 41378

American (AMR) AF: 0.343 AC: 5240 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1411 AN: 5146

South Asian (SAS) AF: 0.377 AC: 1809 AN: 4804

European-Finnish (FIN) AF: 0.397 AC: 4180 AN: 10542

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25390 AN: 67918

Other (OTH) AF: 0.418 AC: 880 AN: 2104

Alfa AF: 0.407 Hom.: 20908

Bravo AF: 0.460

Asia WGS AF: 0.394 AC: 1368 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	9.0
DANN	Benign	0.64
PhyloP100		0.54
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: rs312929; hg19: chr19-3273188;