10-10923586-A-G

Position:

• chr10-10923586-A-G

Variant summary

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

The ENST00000666257.1(LINC00710):​n.1728-5632T>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 0.391 in 152,134 control chromosomes in the GnomAD database, including 13,187 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 0.39 (13187 hom., cov: 32)
• Consequence: LINC00710 ENST00000666257.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.15

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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-20+3587A>G		intron_variant
CELF2	NM_001326318.2	c.-20+3587A>G		intron_variant
CELF2	NM_001326319.2	c.-58+3587A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.1728-5632T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59384 AN: 152016 Hom.: 13147 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.391 AC: 59483 AN: 152134 Hom.: 13187 Cov.: 32 AF XY: 0.397 AC XY: 29490 AN XY: 74374

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.381

Alfa AF: 0.291 Hom.: 9210

Bravo AF: 0.417

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
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: rs2146551; hg19: chr10-10965549;