rs74416793

Variant names:

• chr3-10119143-CAAAAAAAA-C
• rs74416793
• NM_018462.5:c.118+3335_118+3342delAAAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr3-10119143-CAAAAAAAA-C
• chr3-10119143-CAAAAAAAA-CA
• chr3-10119143-CAAAAAAAA-CAAA
• chr3-10119143-CAAAAAAAA-CAAAA
• chr3-10119143-CAAAAAAAA-CAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAAAAAA
• chr3-10119143-CAAAAAAAA-CAAAAAAAAAAAAAA

Variant summary

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

The NM_018462.5(BRK1):​c.118+3335_118+3342delAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000593 in 67,442 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.00059 (0 hom., cov: 26)
• Consequence: BRK1 NM_018462.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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+3335_118+3342delAAAAAAAA		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+3325_118+3332delAAAAAAAA		intron	N/A	ENSP00000432472.1	Q8WUW1-1
	BRK1	ENST00000916415.1		c.178+174_178+181delAAAAAAAA		intron	N/A	ENSP00000586474.1

Frequencies

GnomAD3 genomes AF: 0.000593 AC: 40 AN: 67442 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.0000966

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00121

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000982

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000593 AC: 40 AN: 67442 Hom.: 0 Cov.: 26 AF XY: 0.000698 AC XY: 22 AN XY: 31532

African (AFR) AF: 0.0000966 AC: 2 AN: 20704

American (AMR) AF: 0.00121 AC: 7 AN: 5780

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1632

East Asian (EAS) AF: 0.00 AC: 0 AN: 1766

South Asian (SAS) AF: 0.00 AC: 0 AN: 1866

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2806

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 102

European-Non Finnish (NFE) AF: 0.000982 AC: 31 AN: 31574

Other (OTH) AF: 0.00 AC: 0 AN: 828

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs74416793; hg19: chr3-10160827;