rs9903763

chr17-81070030-T-Cchr17-81070030-T-G

Variant summary

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

The NM_001144888.2(BAIAP2):c.217+12063T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,024 control chromosomes in the GnomAD database, including 15,511 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 0.44 (15511 hom., cov: 32)
• Consequence: BAIAP2 NM_001144888.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

BAIAP2 (HGNC:947): (BAR/IMD domain containing adaptor protein 2) The protein encoded by this gene has been identified as a brain-specific angiogenesis inhibitor (BAI1)-binding protein. This adaptor protein links membrane bound G-proteins to cytoplasmic effector proteins. This protein functions as an insulin receptor tyrosine kinase substrate and suggests a role for insulin in the central nervous system. It also associates with a downstream effector of Rho small G proteins, which is associated with the formation of stress fibers and cytokinesis. This protein is involved in lamellipodia and filopodia formation in motile cells and may affect neuronal growth-cone guidance. This protein has also been identified as interacting with the dentatorubral-pallidoluysian atrophy gene, which is associated with an autosomal dominant neurodegenerative disease. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAIAP2	NM_001144888.2	c.217+12063T>C		intron_variant		ENST00000428708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAIAP2	ENST00000428708.7	c.217+12063T>C		intron_variant		1	NM_001144888.2	A1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67400 AN: 151904 Hom.: 15515 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.443 AC: 67411 AN: 152024 Hom.: 15511 Cov.: 32 AF XY: 0.445 AC XY: 33095 AN XY: 74326

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.442

Alfa AF: 0.342 Hom.: 1054

Bravo AF: 0.434

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	3.2
Dann	Benign	0.63

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: rs9903763; hg19: chr17-79043830;