10-10951863-A-G

Position:

• chr10-10951863-A-G

Variant summary

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

The NR_024411.1(LINC00710):​n.226+75T>C 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 0.174 in 152,438 control chromosomes in the GnomAD database, including 4,068 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 0.17 (4065 hom., cov: 32)
  • Exomes 𝑓: 0.084 (3 hom.)
• Consequence: LINC00710 NR_024411.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00710	NR_024411.1	n.226+75T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.216+75T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26427 AN: 152082 Hom.: 4047 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0293

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.0840 AC: 20 AN: 238 Hom.: 3 Cov.: 0 AF XY: 0.0722 AC XY: 13 AN XY: 180

Gnomad4 AFR exome AF: 0.667

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0619

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.174 AC: 26504 AN: 152200 Hom.: 4065 Cov.: 32 AF XY: 0.171 AC XY: 12695 AN XY: 74444

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.0293

Gnomad4 SAS AF: 0.0404

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.166

Alfa AF: 0.0921 Hom.: 1390

Bravo AF: 0.199

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201071; hg19: chr10-10993826;