3-10116709-A-G

Position:

• chr3-10116709-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018462.5(BRK1):​c.118+890A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,150 control chromosomes in the GnomAD database, including 2,574 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2574 hom., cov: 32)
• Consequence: BRK1 NM_018462.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0170

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 3-10116709-A-G is Benign according to our data. Variant chr3-10116709-A-G is described in ClinVar as [Benign]. Clinvar id is 1249351.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRK1	NM_018462.5	c.118+890A>G		intron_variant		ENST00000530758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRK1	ENST00000530758.2	c.118+890A>G		intron_variant		1	NM_018462.5	P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24844 AN: 152032 Hom.: 2571 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24869 AN: 152150 Hom.: 2574 Cov.: 32 AF XY: 0.160 AC XY: 11924 AN XY: 74406

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.135

Alfa AF: 0.151 Hom.: 334

Bravo AF: 0.173

Asia WGS AF: 0.0920 AC: 322 AN: 3478

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

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.77

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: rs41464050; hg19: chr3-10158393;