rs2243711

Positions:

• chr10-10446842-G-C

Variant summary

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

The NR_120637.1(CELF2-DT):​n.162-12811C>G variant causes a intron, non coding transcript 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 NR_120637.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CELF2-DT	NR_120637.1	n.162-12811C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CELF2-DT	ENST00000670890.2	n.144+15347C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.597

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243711; hg19: chr10-10488805;