rs2146553

chr10-10936303-G-Achr10-10936303-G-Cchr10-10936303-G-T

Variant summary

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

The NR_024411.1(LINC00710):n.458-890C>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 0.666 in 152,190 control chromosomes in the GnomAD database, including 35,460 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 0.67 (35460 hom., cov: 34)
• Consequence: LINC00710 NR_024411.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00710	NR_024411.1	n.458-890C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.1311+321C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101207 AN: 152072 Hom.: 35405 Cov.: 34

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.666 AC: 101317 AN: 152190 Hom.: 35460 Cov.: 34 AF XY: 0.670 AC XY: 49840 AN XY: 74390

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.674

Alfa AF: 0.577 Hom.: 35632

Bravo AF: 0.690

Asia WGS AF: 0.792 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.1
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2146553; hg19: chr10-10978266;