10-10681237-T-C

Position:

• chr10-10681237-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.-132-1219T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0609 in 152,194 control chromosomes in the GnomAD database, including 463 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 0.061 (463 hom., cov: 32)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943

Genes affected

CELF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-94-1219T>C		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-94-1219T>C		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-132-1219T>C		intron_variant			NP_001313248.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9244 AN: 152072 Hom.: 460 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0339

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0609 AC: 9267 AN: 152194 Hom.: 463 Cov.: 32 AF XY: 0.0618 AC XY: 4599 AN XY: 74410

Gnomad4 AFR AF: 0.0955

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.0344

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0355

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.0284 Hom.: 26

Bravo AF: 0.0673

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17148635; hg19: chr10-10723200;