Variant chr11-1411461-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001256627.2(BRSK2):c.91+21086T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 1,470,786 control chromosomes in the GnomAD database, including 166,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.43 ( 14851 hom., cov: 34)

Exomes 𝑓: 0.47 ( 151600 hom. )

Consequence

BRSK2
NM_001256627.2 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0120

Variant links:

Genes affected

BRSK2 (HGNC:11405): (BR serine/threonine kinase 2) Enables several functions, including ATP binding activity; ATPase binding activity; and protein kinase activity. Involved in several processes, including cellular protein metabolic process; intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; and regulation of insulin secretion involved in cellular response to glucose stimulus. Located in centrosome and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

BRSK2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BP6

Variant 11-1411461-T-C is Benign according to our data. Variant chr11-1411461-T-C is described in ClinVar as [Benign]. Clinvar id is 3059255.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRSK2	NM_001256627.2 linkuse as main transcript	c.91+21086T>C		intron_variant		ENST00000528841.6	NP_001243556.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRSK2	ENST00000528841.6 linkuse as main transcript	c.91+21086T>C		intron_variant		1	NM_001256627.2	ENSP00000432000	P1	Q8IWQ3-1

Frequencies

GnomAD3 genomes

AF:

0.428

AC:

65119

AN:

152078

Hom.:

14840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.379

Gnomad AMI

AF:

0.618

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.0204

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.551

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.495

Gnomad OTH

AF:

0.404

GnomAD3 exomes

AF:

0.396

AC:

49994

AN:

126252

Hom.:

11462

AF XY:

0.403

AC XY:

28221

AN XY:

70074

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.309

Gnomad ASJ exome

AF:

0.437

Gnomad EAS exome

AF:

0.0118

Gnomad SAS exome

AF:

0.247

Gnomad FIN exome

AF:

0.536

Gnomad NFE exome

AF:

0.496

Gnomad OTH exome

AF:

0.432

GnomAD4 exome

AF:

0.468

AC:

616859

AN:

1318590

Hom.:

151600

Cov.:

AF XY:

0.463

AC XY:

298314

AN XY:

644582

show subpopulations

Gnomad4 AFR exome

AF:

0.374

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.418

Gnomad4 EAS exome

AF:

0.0160

Gnomad4 SAS exome

AF:

0.263

Gnomad4 FIN exome

AF:

0.534

Gnomad4 NFE exome

AF:

0.503

Gnomad4 OTH exome

AF:

0.438

GnomAD4 genome

AF:

0.428

AC:

65181

AN:

152196

Hom.:

14851

Cov.:

AF XY:

0.423

AC XY:

31503

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.379

Gnomad4 AMR

AF:

0.374

Gnomad4 ASJ

AF:

0.401

Gnomad4 EAS

AF:

0.0209

Gnomad4 SAS

AF:

0.246

Gnomad4 FIN

AF:

0.551

Gnomad4 NFE

AF:

0.495

Gnomad4 OTH

AF:

0.404

Alfa

AF:

0.455

Hom.:

2209

Bravo

AF:

0.412

Asia WGS

AF:

0.146

AC:

511

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BRSK2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

4.7

DANN

Benign

0.44

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