Variant 11-1390271-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001256627.2(BRSK2):c.-14C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 1,009,830 control chromosomes in the GnomAD database, including 191,543 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 21479 hom., cov: 33)

Exomes 𝑓: 0.62 ( 170064 hom. )

Consequence

BRSK2
NM_001256627.2 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0750

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 11-1390271-C-T is Benign according to our data. Variant chr11-1390271-C-T is described in ClinVar as [Benign]. Clinvar id is 1279834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 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.-14C>T		5_prime_UTR_variant	1/20	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.-14C>T		5_prime_UTR_variant	1/20	1	NM_001256627.2	ENSP00000432000	P1	Q8IWQ3-1

Frequencies

GnomAD3 genomes

AF:

0.526

AC:

76954

AN:

146362

Hom.:

21481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.369

Gnomad AMI

AF:

0.566

Gnomad AMR

AF:

0.565

Gnomad ASJ

AF:

0.635

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.420

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.641

Gnomad OTH

AF:

0.590

GnomAD3 exomes

AF:

0.541

AC:

5966

AN:

11032

Hom.:

1705

AF XY:

0.546

AC XY:

3145

AN XY:

5760

show subpopulations

Gnomad AFR exome

AF:

0.442

Gnomad AMR exome

AF:

0.640

Gnomad ASJ exome

AF:

0.737

Gnomad EAS exome

AF:

0.385

Gnomad SAS exome

AF:

0.599

Gnomad FIN exome

AF:

0.461

Gnomad NFE exome

AF:

0.732

Gnomad OTH exome

AF:

0.527

GnomAD4 exome

AF:

0.625

AC:

539275

AN:

863398

Hom.:

170064

Cov.:

AF XY:

0.626

AC XY:

250528

AN XY:

400482

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.600

Gnomad4 ASJ exome

AF:

0.622

Gnomad4 EAS exome

AF:

0.330

Gnomad4 SAS exome

AF:

0.521

Gnomad4 FIN exome

AF:

0.454

Gnomad4 NFE exome

AF:

0.639

Gnomad4 OTH exome

AF:

0.581

GnomAD4 genome

AF:

0.526

AC:

76963

AN:

146432

Hom.:

21479

Cov.:

AF XY:

0.513

AC XY:

36586

AN XY:

71266

show subpopulations

Gnomad4 AFR

AF:

0.368

Gnomad4 AMR

AF:

0.565

Gnomad4 ASJ

AF:

0.635

Gnomad4 EAS

AF:

0.277

Gnomad4 SAS

AF:

0.494

Gnomad4 FIN

AF:

0.420

Gnomad4 NFE

AF:

0.641

Gnomad4 OTH

AF:

0.586

Alfa

AF:

0.437

Hom.:

1219

Bravo

AF:

0.528

Asia WGS

AF:

0.326

AC:

758

AN:

2328

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	Jun 16, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

0.98

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