rs2243711

Variant names:

• chr10-10446842-G-C
• rs2243711
• ENST00000602311.2:n.162-12811C>G

Variant summary

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

The ENST00000602311.2(CELF2-DT):​n.162-12811C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,982 control chromosomes in the GnomAD database, including 27,686 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 0.60 (27686 hom., cov: 32)
• Consequence: CELF2-DT ENST00000602311.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CELF2-DT	NR_120637.1	n.162-12811C>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CELF2-DT	ENST00000602311.2	n.162-12811C>G		intron_variant	Intron 1 of 3	5
CELF2-DT	ENST00000634462.1	n.162-12811C>G		intron_variant	Intron 1 of 2	5
CELF2-DT	ENST00000653741.1	n.132+9461C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91556 AN: 151864 Hom.: 27657 Cov.: 32

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.603 AC: 91635 AN: 151982 Hom.: 27686 Cov.: 32 AF XY: 0.605 AC XY: 44969 AN XY: 74288

African (AFR) AF: 0.621 AC: 25738 AN: 41450

American (AMR) AF: 0.663 AC: 10137 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2226 AN: 3466

East Asian (EAS) AF: 0.575 AC: 2967 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2965 AN: 4814

European-Finnish (FIN) AF: 0.606 AC: 6381 AN: 10528

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39378 AN: 67964

Other (OTH) AF: 0.597 AC: 1262 AN: 2114

Alfa AF: 0.587 Hom.: 3226

Bravo AF: 0.611

Asia WGS AF: 0.598 AC: 2073 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2243711; hg19: chr10-10488805;