rs312932

Positions:

• chr19-3271887-A-C
• chr19-3271887-A-G
• chr19-3271887-A-T

Variant summary

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

The NM_021938.4(CELF5):​c.343-1985A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,044 control chromosomes in the GnomAD database, including 46,742 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 0.78 (46742 hom., cov: 31)
• Consequence: CELF5 NM_021938.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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]

CELF5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF5	NM_021938.4	c.343-1985A>C		intron_variant		ENST00000292672.7	NP_068757.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CELF5	ENST00000292672.7	c.343-1985A>C		intron_variant		1	NM_021938.4	ENSP00000292672.1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117819 AN: 151926 Hom.: 46683 Cov.: 31

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.776 AC: 117942 AN: 152044 Hom.: 46742 Cov.: 31 AF XY: 0.777 AC XY: 57782 AN XY: 74322

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.764

Alfa AF: 0.733 Hom.: 5213

Bravo AF: 0.788

Asia WGS AF: 0.910 AC: 3160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs312932; hg19: chr19-3271885;