chr3-10117393-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018462.5(BRK1):​c.118+1594dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 118,644 control chromosomes in the GnomAD database, including 2,007 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 2007 hom., cov: 21)

Consequence

BRK1
NM_018462.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.931
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 3-10117393-C-CT is Benign according to our data. Variant chr3-10117393-C-CT is described in ClinVar as [Benign]. Clinvar id is 1227437.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRK1NM_018462.5 linkuse as main transcriptc.118+1594dup intron_variant ENST00000530758.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRK1ENST00000530758.2 linkuse as main transcriptc.118+1594dup intron_variant 1 NM_018462.5 P1Q8WUW1-1

Frequencies

GnomAD3 genomes
AF:
0.159
AC:
18877
AN:
118666
Hom.:
2009
Cov.:
21
show subpopulations
Gnomad AFR
AF:
0.245
Gnomad AMI
AF:
0.134
Gnomad AMR
AF:
0.119
Gnomad ASJ
AF:
0.0914
Gnomad EAS
AF:
0.0302
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.0443
Gnomad MID
AF:
0.0968
Gnomad NFE
AF:
0.149
Gnomad OTH
AF:
0.131
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.159
AC:
18873
AN:
118644
Hom.:
2007
Cov.:
21
AF XY:
0.153
AC XY:
8611
AN XY:
56406
show subpopulations
Gnomad4 AFR
AF:
0.245
Gnomad4 AMR
AF:
0.119
Gnomad4 ASJ
AF:
0.0914
Gnomad4 EAS
AF:
0.0301
Gnomad4 SAS
AF:
0.129
Gnomad4 FIN
AF:
0.0443
Gnomad4 NFE
AF:
0.149
Gnomad4 OTH
AF:
0.133

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 07, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs756307171; hg19: chr3-10159077; API