rs992193

chr10-10931353-C-T

Variant summary

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

The ENST00000666257.1(LINC00710):n.1673-1698G>A 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 0.632 in 151,832 control chromosomes in the GnomAD database, including 30,740 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 0.63 (30740 hom., cov: 30)
• Consequence: LINC00710 ENST00000666257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-20+11354C>T		intron_variant
CELF2	NM_001326318.2	c.-20+11354C>T		intron_variant
CELF2	NM_001326319.2	c.-57-9064C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.1673-1698G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95878 AN: 151714 Hom.: 30740 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.632 AC: 95900 AN: 151832 Hom.: 30740 Cov.: 30 AF XY: 0.632 AC XY: 46904 AN XY: 74172

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.683

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.638

Alfa AF: 0.673 Hom.: 46031

Bravo AF: 0.615

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.3
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs992193; hg19: chr10-10973316;