rs2031339

Positions:

• chr10-10544600-T-C

Variant summary

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

The NM_001326319.2(CELF2):​c.-133+82014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,176 control chromosomes in the GnomAD database, including 8,822 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 0.33 (8822 hom., cov: 34)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

Genes affected

CELF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-95+82014T>C		intron_variant
CELF2	NM_001326318.2	c.-95+82014T>C		intron_variant
CELF2	NM_001326319.2	c.-133+82014T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49620 AN: 152058 Hom.: 8827 Cov.: 34

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.326 AC: 49623 AN: 152176 Hom.: 8822 Cov.: 34 AF XY: 0.325 AC XY: 24143 AN XY: 74396

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.339

Alfa AF: 0.374 Hom.: 4831

Bravo AF: 0.313

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2031339; hg19: chr10-10586563;