10-10491192-G-C

Position:

• chr10-10491192-G-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+28606G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,960 control chromosomes in the GnomAD database, including 10,563 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 0.36 (10563 hom., cov: 32)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

CELF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-95+28606G>C		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-95+28606G>C		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-133+28606G>C		intron_variant			NP_001313248.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54572 AN: 151842 Hom.: 10548 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.359 AC: 54625 AN: 151960 Hom.: 10563 Cov.: 32 AF XY: 0.364 AC XY: 27045 AN XY: 74282

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.383

Alfa AF: 0.360 Hom.: 1269

Bravo AF: 0.362

Asia WGS AF: 0.442 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2477037; hg19: chr10-10533155;