rs312932

Variant names:

• chr19-3271887-A-C
• rs312932
• NM_021938.4:c.343-1985A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_021938.4(CELF5):​c.343-1985A>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
• 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=-0.92).
• 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 rank	MANE	Protein	UniProt
CELF5	NM_021938.4	c.343-1985A>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.343-1985A>C		intron_variant	Intron 2 of 12	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

African (AFR) AF: 0.930 AC: 38582 AN: 41502

American (AMR) AF: 0.744 AC: 11348 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2546 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5027 AN: 5180

South Asian (SAS) AF: 0.840 AC: 4035 AN: 4806

European-Finnish (FIN) AF: 0.656 AC: 6924 AN: 10558

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46927 AN: 67948

Other (OTH) AF: 0.764 AC: 1612 AN: 2110

Alfa AF: 0.733 Hom.: 59826

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
PhyloP100		-0.13
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: rs312932; hg19: chr19-3271885;