Variant 3-10118448-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_018462.5(BRK1):c.118+2629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,726 control chromosomes in the GnomAD database, including 2,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2567 hom., cov: 30)

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 Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-10118448-C-T is Benign according to our data. Variant chr3-10118448-C-T is described in ClinVar as [Benign]. Clinvar id is 1262553.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRK1	NM_018462.5 linkuse as main transcript	c.118+2629C>T		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+2629C>T		intron_variant		1	NM_018462.5	P1	Q8WUW1-1

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24785

AN:

151612

Hom.:

2564

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0874

Gnomad EAS

AF:

0.0320

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.0840

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.134

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

GnomAD4 genome

AF:

0.164

AC:

24810

AN:

151726

Hom.:

2567

Cov.:

AF XY:

0.160

AC XY:

11891

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.291

Gnomad4 AMR

AF:

0.129

Gnomad4 ASJ

AF:

0.0874

Gnomad4 EAS

AF:

0.0319

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.0840

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.135

Alfa

AF:

0.139

Hom.:

220

Bravo

AF:

0.173

Asia WGS

AF:

0.0920

AC:

321

AN:

3478

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

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.4

DANN

Benign

0.52

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