Variant 13-45713174-T-C 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_152719.3(CBY2):c.157-8T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000631 in 1,601,310 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00091 ( 3 hom., cov: 33)

Exomes 𝑓: 0.00060 ( 6 hom. )

Consequence

CBY2
NM_152719.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0001009

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.33

Variant links:

Genes affected

CBY2 (HGNC:30720): (chibby family member 2) Enables identical protein binding activity. Predicted to be located in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

CBY2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 13-45713174-T-C is Benign according to our data. Variant chr13-45713174-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2643805.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBY2	NM_152719.3 linkuse as main transcript	c.157-8T>C		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000310521.6	NP_689932.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
CBY2	ENST00000310521.6 linkuse as main transcript	c.157-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_152719.3	ENSP00000309189	P3	Q8NA61-1
CBY2	ENST00000378966.3 linkuse as main transcript	c.49-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000368249	A2	Q8NA61-2
CBY2	ENST00000533564.1 linkuse as main transcript	c.76-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000435230
CBY2	ENST00000610924.1 linkuse as main transcript	c.49-8T>C	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	5		ENSP00000480148	A2	Q8NA61-2

Frequencies

GnomAD3 genomes

AF:

0.000901

AC:

137

AN:

152048

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000725

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00436

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000647

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.000953

AC:

226

AN:

237226

Hom.:

AF XY:

0.00122

AC XY:

157

AN XY:

129082

show subpopulations

Gnomad AFR exome

AF:

0.000131

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.000328

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00409

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000520

Gnomad OTH exome

AF:

0.000515

GnomAD4 exome

AF:

0.000602

AC:

873

AN:

1449144

Hom.:

Cov.:

AF XY:

0.000738

AC XY:

531

AN XY:

719924

show subpopulations

Gnomad4 AFR exome

AF:

0.000150

Gnomad4 AMR exome

AF:

0.00104

Gnomad4 ASJ exome

AF:

0.000237

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00413

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000343

Gnomad4 OTH exome

AF:

0.000769

GnomAD4 genome

AF:

0.000907

AC:

138

AN:

152166

Hom.:

Cov.:

AF XY:

0.00120

AC XY:

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0000722

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00458

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000647

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.000521

Hom.:

Bravo

AF:

0.000642

Asia WGS

AF:

0.00318

AC:

AN:

3478

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

CBY2: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.9

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00010

dbscSNV1_RF

Benign

0.0060

SpliceAI score (max)

0.040

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