17-81050837-G-A

Position:

• chr17-81050837-G-A

Variant summary

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

The NM_001144888.2(BAIAP2):​c.55-2831G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 148,654 control chromosomes in the GnomAD database, including 6,752 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 0.30 (6752 hom., cov: 27)
• Consequence: BAIAP2 NM_001144888.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAIAP2	NM_001144888.2	c.55-2831G>A		intron_variant		ENST00000428708.7	NP_001138360.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAIAP2	ENST00000428708.7	c.55-2831G>A		intron_variant		1	NM_001144888.2	ENSP00000401022	A1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 44106 AN: 148538 Hom.: 6754 Cov.: 27

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.297 AC: 44100 AN: 148654 Hom.: 6752 Cov.: 27 AF XY: 0.297 AC XY: 21610 AN XY: 72672

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.286

Alfa AF: 0.314 Hom.: 9145

Bravo AF: 0.283

Asia WGS AF: 0.241 AC: 839 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.55

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: rs8067235; hg19: chr17-79024637;