chr3-10117393-C-CT

Position:

• chr3-10117393-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.931

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]

ACMG classification

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
BRK1	NM_018462.5	c.118+1594dup		intron_variant		ENST00000530758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRK1	ENST00000530758.2	c.118+1594dup		intron_variant		1	NM_018462.5	P1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 18877 AN: 118666 Hom.: 2009 Cov.: 21

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

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 07, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs756307171; hg19: chr3-10159077;