chr3-10119001-T-TTTTG

Position:

• chr3-10119001-T-TTTTG

Variant summary

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

The NM_018462.5(BRK1):​c.118+3194_118+3197dup 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 151,896 control chromosomes in the GnomAD database, including 2,539 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.16 (2539 hom., cov: 27)
• Consequence: BRK1 NM_018462.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.114

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 3-10119001-T-TTTTG is Benign according to our data. Variant chr3-10119001-T-TTTTG is described in ClinVar as [Benign]. Clinvar id is 1227105.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRK1	NM_018462.5	c.118+3194_118+3197dup		intron_variant		ENST00000530758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRK1	ENST00000530758.2	c.118+3194_118+3197dup		intron_variant		1	NM_018462.5	P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24682 AN: 151778 Hom.: 2536 Cov.: 27

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.163 AC: 24707 AN: 151896 Hom.: 2539 Cov.: 27 AF XY: 0.160 AC XY: 11849 AN XY: 74244

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0826

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.134

Asia WGS AF: 0.0910 AC: 318 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

Aug 15, 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: rs112147329; hg19: chr3-10160685;