Variant chr3-10119143-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_018462.5(BRK1):c.118+3324C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.047 ( 0 hom., cov: 11)

Failed GnomAD Quality Control

Consequence

BRK1
NM_018462.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.212

Variant links:

Genes affected

BRK1 (HGNC:23057): (BRICK1 subunit of SCAR/WAVE actin nucleating complex) Enables identical protein binding activity. Contributes to small GTPase binding activity. Involved in Rac protein signal transduction and positive regulation of cellular component organization. Located in extracellular exosome. Part of SCAR complex. [provided by Alliance of Genome Resources, Apr 2022]

BRK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 3-10119143-C-A is Benign according to our data. Variant chr3-10119143-C-A is described in ClinVar as [Benign]. Clinvar id is 1248233.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRK1	NM_018462.5 linkuse as main transcript	c.118+3324C>A		intron_variant		ENST00000530758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRK1	ENST00000530758.2 linkuse as main transcript	c.118+3324C>A		intron_variant		1	NM_018462.5	P1	Q8WUW1-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

3078

AN:

65306

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0265

Gnomad AMI

AF:

0.0656

Gnomad AMR

AF:

0.0670

Gnomad ASJ

AF:

0.0614

Gnomad EAS

AF:

0.0529

Gnomad SAS

AF:

0.0352

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.106

Gnomad NFE

AF:

0.0500

Gnomad OTH

AF:

0.0495

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0472

AC:

3084

AN:

65332

Hom.:

Cov.:

AF XY:

0.0516

AC XY:

1583

AN XY:

30652

show subpopulations

Gnomad4 AFR

AF:

0.0266

Gnomad4 AMR

AF:

0.0675

Gnomad4 ASJ

AF:

0.0614

Gnomad4 EAS

AF:

0.0529

Gnomad4 SAS

AF:

0.0359

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.0500

Gnomad4 OTH

AF:

0.0489

Alfa

AF:

0.0137

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 01, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.2

DANN

Benign

0.48

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