7-98315621-A-ATAAT

Variant names:

• chr7-98315621-A-ATAAT
• rs201588264
• NM_018842.5:c.487-10_487-9insATTA

Variant summary

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

The NM_018842.5(BAIAP2L1):​c.487-10_487-9insATTA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 9.2e-7 (0 hom.)
• Consequence: BAIAP2L1 NM_018842.5 intron
• Clinical Significance: Not reported in ClinVar
• 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: Uncertain_significance. The variant received 0 ACMG points.

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_487-9insATTA		intron	N/A	NP_061330.2

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 9.20e-7 AC: 1 AN: 1086406 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 531512

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

African (AFR) AF: 0.00 AC: 0 AN: 22710

American (AMR) AF: 0.00 AC: 0 AN: 17982

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16932

East Asian (EAS) AF: 0.00 AC: 0 AN: 29056

South Asian (SAS) AF: 0.00 AC: 0 AN: 35906

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38532

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3380

European-Non Finnish (NFE) AF: 0.00000114 AC: 1 AN: 878412

Other (OTH) AF: 0.00 AC: 0 AN: 43496

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs201588264; hg19: chr7-97944933;