Variant 15-90230807-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006384.4(CIB1):c.554+127G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 887,354 control chromosomes in the GnomAD database, including 41,888 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 6195 hom., cov: 33)

Exomes 𝑓: 0.28 ( 35693 hom. )

Consequence

CIB1
NM_006384.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.754

Variant links:

Genes affected

CIB1 (HGNC:16920): (calcium and integrin binding 1) This gene encodes a member of the EF-hand domain-containing calcium-binding superfamily. The encoded protein interacts with many other proteins, including the platelet integrin alpha-IIb-beta-3, DNA-dependent protein kinase, presenilin-2, focal adhesion kinase, p21 activated kinase, and protein kinase D. The encoded protein may be involved in cell survival and proliferation, and is associated with several disease states including cancer and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

CIB1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 15-90230807-C-T is Benign according to our data. Variant chr15-90230807-C-T is described in ClinVar as [Benign]. Clinvar id is 2688000.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CIB1	NM_006384.4 linkuse as main transcript	c.554+127G>A		intron_variant		ENST00000328649.11	NP_006375.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CIB1	ENST00000328649.11 linkuse as main transcript	c.554+127G>A		intron_variant		1	NM_006384.4	ENSP00000333873	P1	Q99828-1

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40103

AN:

151982

Hom.:

6186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.399

Gnomad ASJ

AF:

0.172

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.423

Gnomad FIN

AF:

0.269

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.234

Gnomad OTH

AF:

0.273

GnomAD4 exome

AF:

0.284

AC:

209135

AN:

735252

Hom.:

35693

AF XY:

0.288

AC XY:

111893

AN XY:

387986

show subpopulations

Gnomad4 AFR exome

AF:

0.191

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.186

Gnomad4 EAS exome

AF:

0.661

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.273

Gnomad4 NFE exome

AF:

0.229

Gnomad4 OTH exome

AF:

0.269

GnomAD4 genome

AF:

0.264

AC:

40130

AN:

152102

Hom.:

6195

Cov.:

AF XY:

0.274

AC XY:

20403

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.399

Gnomad4 ASJ

AF:

0.172

Gnomad4 EAS

AF:

0.695

Gnomad4 SAS

AF:

0.423

Gnomad4 FIN

AF:

0.269

Gnomad4 NFE

AF:

0.234

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.240

Hom.:

732

Bravo

AF:

0.269

Asia WGS

AF:

0.508

AC:

1765

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 74% of patients studied by a panel of primary immunodeficiencies. Number of patients: 70. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.63

DANN

Benign

0.55

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