rs201588264

Variant names:

• chr7-98315621-A-AT
• rs201588264
• NM_018842.5:c.487-10_487-9insA

Your query was ambiguous. Multiple possible variants found:

• chr7-98315621-A-AT
• chr7-98315621-A-ATAAT
• chr7-98315621-A-ATGAT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.653
• Publications: 0 publications found

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]

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]

ACMG classification

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAIAP2L1	NM_018842.5	c.487-10_487-9insA		intron_variant	Intron 6 of 13	ENST00000005260.9	NP_061330.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAIAP2L1	ENST00000005260.9	c.487-10_487-9insA		intron_variant	Intron 6 of 13	1	NM_018842.5	ENSP00000005260.8
BAIAP2L1	ENST00000462558.5	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.: 0

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

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.: 16 AF XY: 0.414 AC XY: 217983 AN XY: 526682

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

GnomAD4 genome AF: 0.366 AC: 54710 AN: 149460 Hom.: 11567 Cov.: 0 AF XY: 0.361 AC XY: 26386 AN XY: 73000

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

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

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
PhyloP100		-0.65
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: rs201588264; hg19: chr7-97944933;