10-10515910-G-T

Position:

• chr10-10515910-G-T

Variant summary

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

The NM_001326319.2(CELF2):​c.-133+53324G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.062 in 152,202 control chromosomes in the GnomAD database, including 465 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 0.062 (465 hom., cov: 32)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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 (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-95+53324G>T		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-95+53324G>T		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-133+53324G>T		intron_variant			NP_001313248.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9425 AN: 152084 Hom.: 468 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.0385

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0517

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

GnomAD4 genome AF: 0.0620 AC: 9430 AN: 152202 Hom.: 465 Cov.: 32 AF XY: 0.0583 AC XY: 4335 AN XY: 74412

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0364

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0378 Hom.: 154

Bravo AF: 0.0670

Asia WGS AF: 0.0420 AC: 146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1000039; hg19: chr10-10557873;