3-10118252-CAAAAAAAAA-CAAAAAAAA

Variant names:

• chr3-10118252-CA-C
• rs59622736
• NM_018462.5:c.118+2451delA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018462.5(BRK1):​c.118+2451delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0092 (1 hom., cov: 27)
  • Failed GnomAD Quality Control
• Consequence: BRK1 NM_018462.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.685
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018462.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRK1	NM_018462.5	MANE Select	c.118+2451delA		intron	N/A	NP_060932.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRK1	ENST00000530758.2	TSL:1 MANE Select	c.118+2434delA		intron	N/A	ENSP00000432472.1	Q8WUW1-1
	BRK1	ENST00000916415.1		c.114-653delA		intron	N/A	ENSP00000586474.1

Frequencies

GnomAD3 genomes AF: 0.00915 AC: 617 AN: 67454 Hom.: 1 Cov.: 27

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00867

Gnomad ASJ AF: 0.00184

Gnomad EAS AF: 0.00301

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00904

Gnomad OTH AF: 0.0101

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00916 AC: 618 AN: 67466 Hom.: 1 Cov.: 27 AF XY: 0.0109 AC XY: 345 AN XY: 31576

African (AFR) AF: 0.00255 AC: 49 AN: 19190

American (AMR) AF: 0.00884 AC: 51 AN: 5768

Ashkenazi Jewish (ASJ) AF: 0.00184 AC: 3 AN: 1628

East Asian (EAS) AF: 0.00302 AC: 6 AN: 1990

South Asian (SAS) AF: 0.00104 AC: 2 AN: 1914

European-Finnish (FIN) AF: 0.0648 AC: 205 AN: 3166

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 98

European-Non Finnish (NFE) AF: 0.00904 AC: 293 AN: 32394

Other (OTH) AF: 0.0100 AC: 9 AN: 898

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs59622736; hg19: chr3-10159936;