chr7-98315625-A-ATAAT

Variant names:

• chr7-98315625-A-ATAAT
• rs372695844
• NM_018842.5:c.487-14_487-13insATTA

Variant summary

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

The NM_018842.5(BAIAP2L1):​c.487-14_487-13insATTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 1,112,614 control chromosomes in the GnomAD database, including 81,653 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (9858 hom., cov: 32)
  • Exomes 𝑓: 0.37 (71795 hom.)
• Consequence: BAIAP2L1 NM_018842.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00
• 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 7-98315625-A-ATAAT is Benign according to our data. Variant chr7-98315625-A-ATAAT is described in ClinVar as Benign. ClinVar VariationId is 402407.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.340 AC: 50709 AN: 149010 Hom.: 9863 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.381

GnomAD2 exomes AF: 0.213 AC: 16363 AN: 76812 AF XY: 0.206

Gnomad AFR exome AF: 0.0688

Gnomad AMR exome AF: 0.105

Gnomad ASJ exome AF: 0.284

Gnomad EAS exome AF: 0.100

Gnomad FIN exome AF: 0.322

Gnomad NFE exome AF: 0.255

Gnomad OTH exome AF: 0.208

GnomAD4 exome AF: 0.373 AC: 359498 AN: 963532 Hom.: 71795 Cov.: 14 AF XY: 0.372 AC XY: 175547 AN XY: 472452

African (AFR) AF: 0.129 AC: 2554 AN: 19758

American (AMR) AF: 0.251 AC: 3925 AN: 15650

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 6557 AN: 15050

East Asian (EAS) AF: 0.192 AC: 5094 AN: 26524

South Asian (SAS) AF: 0.130 AC: 4120 AN: 31700

European-Finnish (FIN) AF: 0.347 AC: 12147 AN: 35026

Middle Eastern (MID) AF: 0.431 AC: 1240 AN: 2880

European-Non Finnish (NFE) AF: 0.399 AC: 310106 AN: 777902

Other (OTH) AF: 0.352 AC: 13755 AN: 39042

GnomAD4 genome AF: 0.340 AC: 50684 AN: 149082 Hom.: 9858 Cov.: 32 AF XY: 0.335 AC XY: 24414 AN XY: 72804

African (AFR) AF: 0.164 AC: 6643 AN: 40494

American (AMR) AF: 0.366 AC: 5487 AN: 14990

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1613 AN: 3452

East Asian (EAS) AF: 0.236 AC: 1212 AN: 5138

South Asian (SAS) AF: 0.171 AC: 817 AN: 4790

European-Finnish (FIN) AF: 0.380 AC: 3617 AN: 9522

Middle Eastern (MID) AF: 0.493 AC: 140 AN: 284

European-Non Finnish (NFE) AF: 0.445 AC: 30021 AN: 67438

Other (OTH) AF: 0.378 AC: 780 AN: 2064

Alfa AF: 0.102 Hom.: 293

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		0.0
Mutation Taster		=9/91	disease causing

Splicing

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

Other links and lift over

dbSNP: rs372695844; hg19: chr7-97944937;