rs11256915

chr10-10922525-G-Achr10-10922525-G-T

Variant summary

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

The ENST00000666257.1(LINC00710):n.1728-4571C>T 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 0.46 in 152,014 control chromosomes in the GnomAD database, including 16,976 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 0.46 (16976 hom., cov: 33)
• Consequence: LINC00710 ENST00000666257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)

CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-20+2526G>A		intron_variant
CELF2	NM_001326318.2	c.-20+2526G>A		intron_variant
CELF2	NM_001326319.2	c.-58+2526G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.1728-4571C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69856 AN: 151896 Hom.: 16979 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.460 AC: 69860 AN: 152014 Hom.: 16976 Cov.: 33 AF XY: 0.457 AC XY: 33970 AN XY: 74308

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.467

Alfa AF: 0.517 Hom.: 10188

Bravo AF: 0.439

Asia WGS AF: 0.362 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.4
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11256915; hg19: chr10-10964488;