dbSNP rs201588264: BAIAP2L1:c.487-10_487-9insA (chr7-98315621-A-AT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018842.5(BAIAP2L1):c.487-10_487-9insA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 11567 hom., cov: 0)

Exomes 𝑓: 0.42 ( 107247 hom. )

Consequence

BAIAP2L1
NM_018842.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.653

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: Benign. The variant received -10 ACMG points.

BP6

Variant 7-98315621-A-AT is Benign according to our data. Variant chr7-98315621-A-AT is described in ClinVar as Benign. ClinVar VariationId is 402406.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018842.5. 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
	BAIAP2L1	NM_018842.5	MANE Select	c.487-10_487-9insA		intron	N/A	NP_061330.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BAIAP2L1	ENST00000005260.9	TSL:1 MANE Select	c.487-10_487-9insA	intron	N/A	ENSP00000005260.8	Q9UHR4
BAIAP2L1	ENST00000462558.5	TSL:1	n.703-10_703-9insA	intron	N/A
BAIAP2L1	ENST00000869917.1		c.502-10_502-9insA	intron	N/A	ENSP00000539976.1

Frequencies

GnomAD3 genomes

AF:

0.366

AC:

54736

AN:

149370

Hom.:

11571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.411

Gnomad MID

AF:

0.526

Gnomad NFE

AF:

0.484

Gnomad OTH

AF:

0.411

GnomAD2 exomes

AF:

0.239

AC:

21754

AN:

90836

AF XY:

0.237

show subpopulations

Gnomad AFR exome

AF:

0.0554

Gnomad AMR exome

AF:

0.120

Gnomad ASJ exome

AF:

0.331

Gnomad EAS exome

AF:

0.0787

Gnomad FIN exome

AF:

0.353

Gnomad NFE exome

AF:

0.308

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.415

AC:

447175

AN:

1076278

Hom.:

107247

Cov.:

AF XY:

0.414

AC XY:

217983

AN XY:

526682

show subpopulations

African (AFR)

AF:

0.133

AC:

2989

AN:

22504

American (AMR)

AF:

0.261

AC:

4666

AN:

17900

Ashkenazi Jewish (ASJ)

AF:

0.478

AC:

8022

AN:

16788

East Asian (EAS)

AF:

0.190

AC:

5498

AN:

28888

South Asian (SAS)

AF:

0.150

AC:

5353

AN:

35744

European-Finnish (FIN)

AF:

0.393

AC:

15054

AN:

38332

Middle Eastern (MID)

AF:

0.480

AC:

1612

AN:

3356

European-Non Finnish (NFE)

AF:

0.445

AC:

387207

AN:

869668

Other (OTH)

AF:

0.389

AC:

16774

AN:

43098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

8942

17884

26827

35769

44711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12166

24332

36498

48664

60830

<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:

0.366

AC:

54710

AN:

149460

Hom.:

11567

Cov.:

AF XY:

0.361

AC XY:

26386

AN XY:

73000

show subpopulations

African (AFR)

AF:

0.172

AC:

6963

AN:

40532

American (AMR)

AF:

0.387

AC:

5825

AN:

15046

Ashkenazi Jewish (ASJ)

AF:

0.507

AC:

1752

AN:

3454

East Asian (EAS)

AF:

0.240

AC:

1240

AN:

5156

South Asian (SAS)

AF:

0.194

AC:

934

AN:

4806

European-Finnish (FIN)

AF:

0.411

AC:

3978

AN:

9686

Middle Eastern (MID)

AF:

0.535

AC:

152

AN:

284

European-Non Finnish (NFE)

AF:

0.484

AC:

32646

AN:

67504

Other (OTH)

AF:

0.407

AC:

849

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1597

3195

4792

6390

7987

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.406

Hom.:

356

Asia WGS

AF:

0.203

AC:

705

AN:

3472

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.65

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over