chr10-10647639-C-T

Position:

• chr10-10647639-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.-132-34817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,090 control chromosomes in the GnomAD database, including 3,439 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 0.20 (3439 hom., cov: 32)
• Consequence: CELF2 NM_001326319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16

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 (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CELF2	NM_001326317.2	c.-94-34817C>T		intron_variant			NP_001313246.1
CELF2	NM_001326318.2	c.-94-34817C>T		intron_variant			NP_001313247.1
CELF2	NM_001326319.2	c.-132-34817C>T		intron_variant			NP_001313248.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29945 AN: 151972 Hom.: 3441 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.197 AC: 29943 AN: 152090 Hom.: 3439 Cov.: 32 AF XY: 0.194 AC XY: 14394 AN XY: 74342

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.201

Alfa AF: 0.226 Hom.: 687

Bravo AF: 0.184

Asia WGS AF: 0.0630 AC: 222 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	0.055
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7092313; hg19: chr10-10689602;