rs10508407

chr10-10582466-C-Achr10-10582466-C-Gchr10-10582466-C-T

Variant summary

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

The NM_001326319.2(CELF2):c.-132-99990C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,880 control chromosomes in the GnomAD database, including 7,982 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 0.32 (7982 hom., cov: 32)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

Genes affected

CELF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-94-99990C>A		intron_variant
CELF2	NM_001326318.2	c.-94-99990C>A		intron_variant
CELF2	NM_001326319.2	c.-132-99990C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47954 AN: 151762 Hom.: 7971 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.316 AC: 48008 AN: 151880 Hom.: 7982 Cov.: 32 AF XY: 0.324 AC XY: 24017 AN XY: 74234

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.315

Alfa AF: 0.202 Hom.: 601

Bravo AF: 0.312

Asia WGS AF: 0.478 AC: 1660 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.19
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508407; hg19: chr10-10624429;