Genetic Variant CELF2:c.146+9G>A (chr10-10920008-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001326325.2(CELF2):c.146+9G>A variant causes a intron 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

CELF2
NM_001326325.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.12

Publications

1 publications found

Variant links:

Genes affected

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 links:

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

LINC00710 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001326325.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
CELF2	NM_001326325.2	c.146+9G>A	intron	N/A	NP_001313254.1
CELF2	NM_001326327.2	c.89+9G>A	intron	N/A	NP_001313256.1	A0A1B0GUN8
CELF2	NM_001326326.2	c.89+9G>A	intron	N/A	NP_001313255.1	A0A1B0GU44

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CELF2	ENST00000637215.1	TSL:5	c.89+9G>A	intron	N/A	ENSP00000490185.1	A0A1B0GUN8
CELF2	ENST00000636488.1	TSL:5	c.89+9G>A	intron	N/A	ENSP00000489955.1	A0A1B0GU44
CELF2	ENST00000638035.1	TSL:5	c.-20+9G>A	intron	N/A	ENSP00000490401.1	O95319-2

Frequencies

GnomAD3 genomes

AF:

0.298

AC:

45274

AN:

151940

Hom.:

7544

Cov.:

show subpopulations

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.:

AF XY:

0.257

AC XY:

130453

AN XY:

508354

show subpopulations

African (AFR)

AF:

0.286

AC:

6564

AN:

22918

American (AMR)

AF:

0.487

AC:

4100

AN:

8416

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

3622

AN:

14372

East Asian (EAS)

AF:

0.701

AC:

18582

AN:

26492

South Asian (SAS)

AF:

0.330

AC:

6412

AN:

19426

European-Finnish (FIN)

AF:

0.267

AC:

5622

AN:

21092

Middle Eastern (MID)

AF:

0.267

AC:

778

AN:

2910

European-Non Finnish (NFE)

AF:

0.238

AC:

218061

AN:

917490

Other (OTH)

AF:

0.286

AC:

12470

AN:

43578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

8662

17324

25987

34649

43311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8756

17512

26268

35024

43780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.298

AC:

45321

AN:

152058

Hom.:

7556

Cov.:

AF XY:

0.306

AC XY:

22746

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.295

AC:

12243

AN:

41474

American (AMR)

AF:

0.424

AC:

6475

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

887

AN:

3464

East Asian (EAS)

AF:

0.701

AC:

3632

AN:

5178

South Asian (SAS)

AF:

0.348

AC:

1678

AN:

4820

European-Finnish (FIN)

AF:

0.285

AC:

3004

AN:

10548

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16480

AN:

67986

Other (OTH)

AF:

0.300

AC:

633

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1585

3169

4754

6338

7923

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

454

908

1362

1816

2270

<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:

0.272

Hom.:

743

Bravo

AF:

0.314

Asia WGS

AF:

0.512

AC:

1781

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.8

(source)

DANN

Benign

0.70

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over