chr3-10118252-C-A

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+2433C>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 0.053 ( 0 hom., cov: 10)
Failed GnomAD Quality Control

Consequence

BRK1
NM_018462.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.619
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]

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=-0.9).
BP6
Variant 3-10118252-C-A is Benign according to our data. Variant chr3-10118252-C-A is described in ClinVar as [Benign]. Clinvar id is 1238958.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRK1NM_018462.5 linkuse as main transcriptc.118+2433C>A intron_variant ENST00000530758.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRK1ENST00000530758.2 linkuse as main transcriptc.118+2433C>A intron_variant 1 NM_018462.5 P1Q8WUW1-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
3459
AN:
64854
Hom.:
0
Cov.:
10
FAILED QC
Gnomad AFR
AF:
0.0348
Gnomad AMI
AF:
0.0842
Gnomad AMR
AF:
0.0542
Gnomad ASJ
AF:
0.0723
Gnomad EAS
AF:
0.0738
Gnomad SAS
AF:
0.0590
Gnomad FIN
AF:
0.0474
Gnomad MID
AF:
0.0714
Gnomad NFE
AF:
0.0615
Gnomad OTH
AF:
0.0726
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:
0.0533
AC:
3459
AN:
64866
Hom.:
0
Cov.:
10
AF XY:
0.0526
AC XY:
1607
AN XY:
30536
show subpopulations
Gnomad4 AFR
AF:
0.0347
Gnomad4 AMR
AF:
0.0542
Gnomad4 ASJ
AF:
0.0723
Gnomad4 EAS
AF:
0.0740
Gnomad4 SAS
AF:
0.0598
Gnomad4 FIN
AF:
0.0474
Gnomad4 NFE
AF:
0.0615
Gnomad4 OTH
AF:
0.0719
Alfa
AF:
0.0994
Hom.:
0

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 submitterclinical testingGeneDxAug 15, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.6
DANN
Benign
0.72

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.

Other links and lift over

dbSNP: rs1177674519; hg19: chr3-10159936; API