chr3-10119143-C-CAA

Position:

• chr3-10119143-C-CAA

Variant summary

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

The NM_018462.5(BRK1):​c.118+3341_118+3342dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0475 in 67,304 control chromosomes in the GnomAD database, including 78 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.047 (78 hom., cov: 26)
• Consequence: BRK1 NM_018462.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.240

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 3-10119143-C-CAA is Benign according to our data. Variant chr3-10119143-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1249200.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRK1	NM_018462.5	c.118+3341_118+3342dup		intron_variant		ENST00000530758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRK1	ENST00000530758.2	c.118+3341_118+3342dup		intron_variant		1	NM_018462.5	P1

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 3196 AN: 67276 Hom.: 78 Cov.: 26

Gnomad AFR AF: 0.0602

Gnomad AMI AF: 0.0421

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0417

Gnomad EAS AF: 0.000569

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.00428

Gnomad MID AF: 0.0294

Gnomad NFE AF: 0.0418

Gnomad OTH AF: 0.0533

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

GnomAD4 genome AF: 0.0475 AC: 3194 AN: 67304 Hom.: 78 Cov.: 26 AF XY: 0.0473 AC XY: 1488 AN XY: 31472

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.0656

Gnomad4 ASJ AF: 0.0417

Gnomad4 EAS AF: 0.000569

Gnomad4 SAS AF: 0.0609

Gnomad4 FIN AF: 0.00428

Gnomad4 NFE AF: 0.0418

Gnomad4 OTH AF: 0.0526

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 19, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs74416793; hg19: chr3-10160827;