Variant chr10-10846131-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001326325.2(CELF2):c.85G>A(p.Asp29Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00356 in 984,760 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0037 ( 6 hom. )

Consequence

CELF2
NM_001326325.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.497

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 10-10846131-G-A is Benign according to our data. Variant chr10-10846131-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640297.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 446 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
CELF2	NM_001326325.2 link	c.85G>A	p.Asp29Asn	missense_variant	2/16	NP_001313254.1
CELF2	XM_047424482.1 link	c.85G>A	p.Asp29Asn	missense_variant	2/16	XP_047280438.1
CELF2	XM_047424483.1 link	c.85G>A	p.Asp29Asn	missense_variant	2/16	XP_047280439.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
CELF2	ENST00000638035 link	c.-81G>A	5_prime_UTR_variant	2/15	5	ENSP00000490401.1	O95319-2
CELF2	ENST00000637215.1 link	c.53+47314G>A	intron_variant		5	ENSP00000490185.1	A0A1B0GUN8
CELF2	ENST00000636488.1 link	c.53+47314G>A	intron_variant		5	ENSP00000489955.1	A0A1B0GU44

Frequencies

GnomAD3 genomes

AF:

0.00293

AC:

446

AN:

152020

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000556

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.000579

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00859

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00397

Gnomad OTH

AF:

0.00335

GnomAD4 exome

AF:

0.00368

AC:

3060

AN:

832622

Hom.:

Cov.:

AF XY:

0.00359

AC XY:

1379

AN XY:

384544

show subpopulations

Gnomad4 AFR exome

AF:

0.000444

Gnomad4 AMR exome

AF:

0.00102

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00280

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00385

Gnomad4 OTH exome

AF:

0.00268

GnomAD4 genome

AF:

0.00293

AC:

446

AN:

152138

Hom.:

Cov.:

AF XY:

0.00292

AC XY:

217

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.000554

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.000581

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00859

Gnomad4 NFE

AF:

0.00397

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.000366

Hom.:

Bravo

AF:

0.00253

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

CELF2: BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.5

DANN

Benign

0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over