3-10118252-C-CAAAAAA

Variant summary

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

The NM_018462.5(BRK1):​c.118+2446_118+2451dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 66,588 control chromosomes in the GnomAD database, including 150 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.092 ( 150 hom., cov: 27)

Consequence

BRK1
NM_018462.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.685
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 Benign. Variant got -10 ACMG points.

BP6
Variant 3-10118252-C-CAAAAAA is Benign according to our data. Variant chr3-10118252-C-CAAAAAA is described in ClinVar as [Benign]. Clinvar id is 1250650.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRK1NM_018462.5 linkuse as main transcriptc.118+2446_118+2451dup intron_variant ENST00000530758.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRK1ENST00000530758.2 linkuse as main transcriptc.118+2446_118+2451dup intron_variant 1 NM_018462.5 P1Q8WUW1-1

Frequencies

GnomAD3 genomes
AF:
0.0917
AC:
6105
AN:
66576
Hom.:
150
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.0455
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.0757
Gnomad ASJ
AF:
0.0994
Gnomad EAS
AF:
0.00906
Gnomad SAS
AF:
0.0513
Gnomad FIN
AF:
0.0423
Gnomad MID
AF:
0.0686
Gnomad NFE
AF:
0.133
Gnomad OTH
AF:
0.0797
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0916
AC:
6102
AN:
66588
Hom.:
150
Cov.:
27
AF XY:
0.0850
AC XY:
2646
AN XY:
31140
show subpopulations
Gnomad4 AFR
AF:
0.0455
Gnomad4 AMR
AF:
0.0755
Gnomad4 ASJ
AF:
0.0994
Gnomad4 EAS
AF:
0.00909
Gnomad4 SAS
AF:
0.0515
Gnomad4 FIN
AF:
0.0423
Gnomad4 NFE
AF:
0.133
Gnomad4 OTH
AF:
0.0790

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 16, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs59622736; hg19: chr3-10159936; API