10-10346232-C-T

Variant names:

• chr10-10346232-C-T
• rs7092703
• ENST00000716844.1:n.416-5039G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716844.1(CELF2-DT):​n.416-5039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,968 control chromosomes in the GnomAD database, including 10,032 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 0.35 (10032 hom., cov: 32)
• Consequence: CELF2-DT ENST00000716844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 3 publications found

Genes affected

CELF2-DT (HGNC:54157): (CELF2 divergent transript)

ENSG00000296323 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF2-DT	ENST00000716844.1	n.416-5039G>A		intron_variant	Intron 2 of 6
CELF2-DT	ENST00000716845.1	n.254-5039G>A		intron_variant	Intron 1 of 3
CELF2-DT	ENST00000716846.1	n.275-8323G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53269 AN: 151850 Hom.: 10032 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.351 AC: 53275 AN: 151968 Hom.: 10032 Cov.: 32 AF XY: 0.355 AC XY: 26373 AN XY: 74302

African (AFR) AF: 0.209 AC: 8655 AN: 41418

American (AMR) AF: 0.355 AC: 5414 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1386 AN: 5160

South Asian (SAS) AF: 0.419 AC: 2019 AN: 4814

European-Finnish (FIN) AF: 0.454 AC: 4800 AN: 10584

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.413 AC: 28036 AN: 67948

Other (OTH) AF: 0.376 AC: 794 AN: 2110

Alfa AF: 0.331 Hom.: 4769

Bravo AF: 0.334

Asia WGS AF: 0.332 AC: 1153 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	0.49
DANN	Benign	0.41
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7092703; hg19: chr10-10388195;