Genetic Variant BAIAP2L1:c.487-14_487-13insA (chr7-98315625-A-AT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_018842.5(BAIAP2L1):c.487-14_487-13insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000798 in 149,172 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00080 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 58 hom. )

Failed GnomAD Quality Control

Consequence

BAIAP2L1
NM_018842.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

0 publications found

Variant links:

Genes affected

BAIAP2L1 (HGNC:21649): (BAR/IMD domain containing adaptor protein 2 like 1) This gene encodes a member of the IMD (IRSp53/MIM homology domain) family. Members of this family can be subdivided in two groups, the IRSp53-like and MIM-like, based on the presence or absence of the SH3 (Src homology 3) domain. The protein encoded by this gene contains a conserved IMD, also known as F-actin bundling domain, at the N-terminus, and a canonical SH3 domain near the C-terminus, so it belongs to the IRSp53-like group. This protein is the substrate for insulin receptor tyrosine kinase and binds to the small GTPase Rac. It is involved in signal transduction pathways that link deformation of the plasma membrane and remodeling of the actin cytoskeleton. It also promotes actin assembly and membrane protrusions when overexpressed in mammalian cells, and is essential to the formation of a potent actin assembly complex during EHEC (Enterohemorrhagic Escherichia coli) pedestal formation. [provided by RefSeq, Oct 2009]

BAIAP2L1 links:

BRI3 (HGNC:1109): (brain protein I3) Enables identical protein binding activity. Predicted to be located in azurophil granule membrane and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

BRI3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAIAP2L1	NM_018842.5 link	c.487-14_487-13insA		intron_variant	Intron 6 of 13	ENST00000005260.9	NP_061330.2	Q9UHR4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAIAP2L1	ENST00000005260.9 link	c.487-14_487-13insA		intron_variant	Intron 6 of 13	1	NM_018842.5	ENSP00000005260.8		Q9UHR4
BAIAP2L1	ENST00000462558.5 link	n.703-14_703-13insA		intron_variant	Intron 6 of 9	1

Frequencies

GnomAD3 genomes

AF:

0.000785

AC:

117

AN:

149098

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000915

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000667

Gnomad ASJ

AF:

0.00376

Gnomad EAS

AF:

0.00233

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.000419

Gnomad MID

AF:

0.00645

Gnomad NFE

AF:

0.000548

Gnomad OTH

AF:

0.000488

GnomAD2 exomes

AF:

0.00448

AC:

344

AN:

76812

AF XY:

0.00446

show subpopulations

Gnomad AFR exome

AF:

0.00190

Gnomad AMR exome

AF:

0.00172

Gnomad ASJ exome

AF:

0.00894

Gnomad EAS exome

AF:

0.00126

Gnomad FIN exome

AF:

0.00366

Gnomad NFE exome

AF:

0.00602

Gnomad OTH exome

AF:

0.00658

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00327

AC:

3173

AN:

971040

Hom.:

Cov.:

AF XY:

0.00325

AC XY:

1545

AN XY:

475662

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00186

AC:

AN:

19882

American (AMR)

AF:

0.00320

AC:

AN:

15642

Ashkenazi Jewish (ASJ)

AF:

0.00814

AC:

122

AN:

14994

East Asian (EAS)

AF:

0.00229

AC:

AN:

26644

South Asian (SAS)

AF:

0.00194

AC:

AN:

31910

European-Finnish (FIN)

AF:

0.00390

AC:

135

AN:

34642

Middle Eastern (MID)

AF:

0.00656

AC:

AN:

2896

European-Non Finnish (NFE)

AF:

0.00323

AC:

2532

AN:

785102

Other (OTH)

AF:

0.00394

AC:

155

AN:

39328

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.308

Heterozygous variant carriers

286

571

857

1142

1428

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

180

270

360

450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000798

AC:

119

AN:

149172

Hom.:

Cov.:

AF XY:

0.000851

AC XY:

AN XY:

72868

show subpopulations

African (AFR)

AF:

0.000913

AC:

AN:

40520

American (AMR)

AF:

0.000666

AC:

AN:

15008

Ashkenazi Jewish (ASJ)

AF:

0.00376

AC:

AN:

3456

East Asian (EAS)

AF:

0.00234

AC:

AN:

5138

South Asian (SAS)

AF:

0.000626

AC:

AN:

4794

European-Finnish (FIN)

AF:

0.000419

AC:

AN:

9546

Middle Eastern (MID)

AF:

0.00704

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.000549

AC:

AN:

67450

Other (OTH)

AF:

0.000484

AC:

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000184

Hom.:

293

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over