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

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAIAP2L1	NM_018842.5 link	c.487-10_487-9insA		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.487-10_487-9insA		intron_variant	Intron 6 of 13	1	NM_018842.5	ENSP00000005260.8		Q9UHR4
BAIAP2L1	ENST00000462558.5 link	n.703-10_703-9insA		intron_variant	Intron 6 of 9	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

GnomAD3 exomes

AF:

0.239

AC:

21754

AN:

90836

Hom.:

5761

AF XY:

0.237

AC XY:

12174

AN XY:

51378

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 SAS exome

AF:

0.0780

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

Gnomad4 AFR exome

AF:

0.133

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.478

Gnomad4 EAS exome

AF:

0.190

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.393

Gnomad4 NFE exome

AF:

0.445

Gnomad4 OTH exome

AF:

0.389

GnomAD4 genome

AF:

0.366

AC:

54710

AN:

149460

Hom.:

11567

Cov.:

AF XY:

0.361

AC XY:

26386

AN XY:

73000

show subpopulations

Gnomad4 AFR

AF:

0.172

Gnomad4 AMR

AF:

0.387

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.240

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.411

Gnomad4 NFE

AF:

0.484

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.406

Hom.:

356

Asia WGS

AF:

0.203

AC:

705

AN:

3472

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over