Variant chr18-72538166-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182511.4(CBLN2):c.*10C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.023 in 1,613,870 control chromosomes in the GnomAD database, including 5,357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 673 hom., cov: 32)

Exomes 𝑓: 0.022 ( 4684 hom. )

Consequence

CBLN2
NM_182511.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.867

Variant links:

Genes affected

CBLN2 (HGNC:1544): (cerebellin 2 precursor) Predicted to be involved in maintenance of synapse structure and spontaneous synaptic transmission. Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in extracellular space. Predicted to be active in glutamatergic synapse. [provided by Alliance of Genome Resources, Apr 2022]

CBLN2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 18-72538166-G-A is Benign according to our data. Variant chr18-72538166-G-A is described in ClinVar as [Benign]. Clinvar id is 1284185.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBLN2	NM_182511.4 linkuse as main transcript	c.*10C>T		3_prime_UTR_variant	5/5	ENST00000269503.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBLN2	ENST00000269503.9 linkuse as main transcript	c.*10C>T		3_prime_UTR_variant	5/5	1	NM_182511.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0312

AC:

4738

AN:

151950

Hom.:

672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0112

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0352

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.483

Gnomad SAS

AF:

0.0455

Gnomad FIN

AF:

0.0650

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00407

Gnomad OTH

AF:

0.0292

GnomAD3 exomes

AF:

0.0535

AC:

13442

AN:

251394

Hom.:

2415

AF XY:

0.0500

AC XY:

6796

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.0117

Gnomad AMR exome

AF:

0.0366

Gnomad ASJ exome

AF:

0.00288

Gnomad EAS exome

AF:

0.498

Gnomad SAS exome

AF:

0.0302

Gnomad FIN exome

AF:

0.0594

Gnomad NFE exome

AF:

0.00373

Gnomad OTH exome

AF:

0.0262

GnomAD4 exome

AF:

0.0221

AC:

32331

AN:

1461802

Hom.:

4684

Cov.:

AF XY:

0.0220

AC XY:

16007

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.00893

Gnomad4 AMR exome

AF:

0.0347

Gnomad4 ASJ exome

AF:

0.00302

Gnomad4 EAS exome

AF:

0.462

Gnomad4 SAS exome

AF:

0.0310

Gnomad4 FIN exome

AF:

0.0577

Gnomad4 NFE exome

AF:

0.00380

Gnomad4 OTH exome

AF:

0.0341

GnomAD4 genome

AF:

0.0312

AC:

4746

AN:

152068

Hom.:

673

Cov.:

AF XY:

0.0367

AC XY:

2725

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.0113

Gnomad4 AMR

AF:

0.0352

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.484

Gnomad4 SAS

AF:

0.0455

Gnomad4 FIN

AF:

0.0650

Gnomad4 NFE

AF:

0.00407

Gnomad4 OTH

AF:

0.0308

Alfa

AF:

0.00902

Hom.:

Bravo

AF:

0.0310

Asia WGS

AF:

0.197

AC:

683

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 06, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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