dbSNP rs201071: LINC00710:n.275+75T>C (chr10-10951863-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000428520.7(LINC00710):n.275+75T>C variant causes a intron 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
ENST00000428520.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118

Publications

2 publications found

Variant links:

Genes affected

LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)

LINC00710 links:

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]

CELF2 Gene-Disease associations (from GenCC):

developmental and epileptic encephalopathy 97
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
undetermined early-onset epileptic encephalopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
complex neurodevelopmental disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

CELF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	Protein
CELF2	NM_001326325.2 link	c.146+31864A>G	intron_variant	Intron 3 of 15	NP_001313254.1
CELF2	NM_001326327.2 link	c.89+31864A>G	intron_variant	Intron 2 of 14	NP_001313256.1
CELF2	NM_001326326.2 link	c.89+31864A>G	intron_variant	Intron 2 of 14	NP_001313255.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00710	ENST00000428520.7 link	n.275+75T>C	intron_variant	Intron 1 of 5	1
LINC00710	ENST00000635670.2 link	n.224+75T>C	intron_variant	Intron 1 of 4	1
LINC00710	ENST00000450174.2 link	n.233T>C	non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26427

AN:

152082

Hom.:

4047

Cov.:

show subpopulations

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:

AN:

238

Hom.:

Cov.:

AF XY:

0.0722

AC XY:

AN XY:

180

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0619

AC:

AN:

210

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.436

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.174

AC:

26504

AN:

152200

Hom.:

4065

Cov.:

AF XY:

0.171

AC XY:

12695

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.392

AC:

16278

AN:

41496

American (AMR)

AF:

0.242

AC:

3692

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0787

AC:

273

AN:

3470

East Asian (EAS)

AF:

0.0293

AC:

152

AN:

5180

South Asian (SAS)

AF:

0.0404

AC:

195

AN:

4826

European-Finnish (FIN)

AF:

0.0347

AC:

368

AN:

10612

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0745

AC:

5067

AN:

68018

Other (OTH)

AF:

0.166

AC:

350

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

937

1874

2810

3747

4684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0961

Hom.:

1852

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

(source)

DANN

Benign

0.72

PhyloP100

-0.12

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over