10-10920008-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000666257.1(LINC00710):n.1728-2054C>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 0.262 in 1,228,752 control chromosomes in the GnomAD database, including 46,622 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (7556 hom., cov: 32)
  • Exomes 𝑓: 0.26 (39066 hom.)
• Consequence: LINC00710 ENST00000666257.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.12

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 10-10920008-G-A is Benign according to our data. Variant chr10-10920008-G-A is described in ClinVar as [Benign]. Clinvar id is 769767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CELF2	NM_001326317.2	c.-20+9G>A		intron_variant
CELF2	NM_001326318.2	c.-20+9G>A		intron_variant
CELF2	NM_001326319.2	c.-58+9G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00710	ENST00000666257.1	n.1728-2054C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45274 AN: 151940 Hom.: 7544 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.257 AC: 276211 AN: 1076694 Hom.: 39066 Cov.: 29 AF XY: 0.257 AC XY: 130453 AN XY: 508354

Gnomad4 AFR exome AF: 0.286

Gnomad4 AMR exome AF: 0.487

Gnomad4 ASJ exome AF: 0.252

Gnomad4 EAS exome AF: 0.701

Gnomad4 SAS exome AF: 0.330

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.238

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.298 AC: 45321 AN: 152058 Hom.: 7556 Cov.: 32 AF XY: 0.306 AC XY: 22746 AN XY: 74344

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.300

Alfa AF: 0.272 Hom.: 714

Bravo AF: 0.314

Asia WGS AF: 0.512 AC: 1781 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11256914; hg19: chr10-10961971;