rs9649213

Positions:

• chr7-98391899-A-G
• chr7-98391899-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018842.5(BAIAP2L1):​c.51+8903T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,712 control chromosomes in the GnomAD database, including 14,461 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (14461 hom., cov: 30)
• Consequence: BAIAP2L1 NM_018842.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAIAP2L1	NM_018842.5	c.51+8903T>C		intron_variant		ENST00000005260.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAIAP2L1	ENST00000005260.9	c.51+8903T>C		intron_variant		1	NM_018842.5	P1
BAIAP2L1	ENST00000462558.5	n.267+8903T>C		intron_variant, non_coding_transcript_variant		1
BAIAP2L1	ENST00000479789.1	n.357+8082T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64002 AN: 151594 Hom.: 14428 Cov.: 30

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.396

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.422 AC: 64082 AN: 151712 Hom.: 14461 Cov.: 30 AF XY: 0.425 AC XY: 31517 AN XY: 74130

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.397

Alfa AF: 0.338 Hom.: 15628

Bravo AF: 0.427

Asia WGS AF: 0.500 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.27

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

Other links and lift over

dbSNP: rs9649213; hg19: chr7-98021211; COSMIC: COSV50054709;