3-10116618-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018462.5(BRK1):​c.118+799C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,004 control chromosomes in the GnomAD database, including 5,329 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 5329 hom., cov: 32)

Consequence

BRK1
NM_018462.5 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.551
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 3-10116618-C-G is Benign according to our data. Variant chr3-10116618-C-G is described in ClinVar as [Benign]. Clinvar id is 1277703.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRK1NM_018462.5 linkuse as main transcriptc.118+799C>G intron_variant ENST00000530758.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRK1ENST00000530758.2 linkuse as main transcriptc.118+799C>G intron_variant 1 NM_018462.5 P1Q8WUW1-1

Frequencies

GnomAD3 genomes
AF:
0.233
AC:
35432
AN:
151886
Hom.:
5322
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.431
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.167
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.0934
Gnomad SAS
AF:
0.220
Gnomad FIN
AF:
0.116
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.200
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.233
AC:
35475
AN:
152004
Hom.:
5329
Cov.:
32
AF XY:
0.228
AC XY:
16945
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.431
Gnomad4 AMR
AF:
0.167
Gnomad4 ASJ
AF:
0.151
Gnomad4 EAS
AF:
0.0932
Gnomad4 SAS
AF:
0.220
Gnomad4 FIN
AF:
0.116
Gnomad4 NFE
AF:
0.163
Gnomad4 OTH
AF:
0.200
Alfa
AF:
0.202
Hom.:
465
Bravo
AF:
0.248
Asia WGS
AF:
0.154
AC:
538
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 submitterclinical testingGeneDxJul 06, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
7.0
DANN
Benign
0.79

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: rs17032414; hg19: chr3-10158302; API