Variant 17-81035353-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001144888.2(BAIAP2):c.54+45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 1,231,708 control chromosomes in the GnomAD database, including 502,910 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.88 ( 57981 hom., cov: 31)

Exomes 𝑓: 0.91 ( 444929 hom. )

Consequence

BAIAP2
NM_001144888.2 intron

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.53

Variant links:

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]

BAIAP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAIAP2	NM_001144888.2 link	c.54+45T>C		intron_variant	Intron 1 of 13	ENST00000428708.7	NP_001138360.1	Q9UQB8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAIAP2	ENST00000428708.7 link	c.54+45T>C		intron_variant	Intron 1 of 13	1	NM_001144888.2	ENSP00000401022.2		Q9UQB8-2

Frequencies

GnomAD3 genomes

AF:

0.884

AC:

130896

AN:

148152

Hom.:

57949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.864

Gnomad AMR

AF:

0.918

Gnomad ASJ

AF:

0.897

Gnomad EAS

AF:

0.936

Gnomad SAS

AF:

0.936

Gnomad FIN

AF:

0.904

Gnomad MID

AF:

0.913

Gnomad NFE

AF:

0.905

Gnomad OTH

AF:

0.873

GnomAD3 exomes

AF:

0.901

AC:

54029

AN:

59956

Hom.:

24368

AF XY:

0.903

AC XY:

32057

AN XY:

35488

show subpopulations

Gnomad AFR exome

AF:

0.771

Gnomad AMR exome

AF:

0.921

Gnomad ASJ exome

AF:

0.881

Gnomad EAS exome

AF:

0.874

Gnomad SAS exome

AF:

0.919

Gnomad FIN exome

AF:

0.906

Gnomad NFE exome

AF:

0.897

Gnomad OTH exome

AF:

0.906

GnomAD4 exome

AF:

0.906

AC:

981505

AN:

1083448

Hom.:

444929

Cov.:

AF XY:

0.906

AC XY:

479152

AN XY:

528830

show subpopulations

Gnomad4 AFR exome

AF:

0.803

Gnomad4 AMR exome

AF:

0.920

Gnomad4 ASJ exome

AF:

0.885

Gnomad4 EAS exome

AF:

0.930

Gnomad4 SAS exome

AF:

0.920

Gnomad4 FIN exome

AF:

0.902

Gnomad4 NFE exome

AF:

0.908

Gnomad4 OTH exome

AF:

0.905

GnomAD4 genome

AF:

0.883

AC:

130977

AN:

148260

Hom.:

57981

Cov.:

AF XY:

0.885

AC XY:

63984

AN XY:

72262

show subpopulations

Gnomad4 AFR

AF:

0.818

Gnomad4 AMR

AF:

0.918

Gnomad4 ASJ

AF:

0.897

Gnomad4 EAS

AF:

0.936

Gnomad4 SAS

AF:

0.936

Gnomad4 FIN

AF:

0.904

Gnomad4 NFE

AF:

0.905

Gnomad4 OTH

AF:

0.875

Alfa

AF:

0.893

Hom.:

7554

Bravo

AF:

0.883

Asia WGS

AF:

0.927

AC:

3054

AN:

3296

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Attention deficit hyperactivity disorder

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Gene Variants in BAIAP2 have been studied in several populations and are known to cause ADHD. Potent variants of this gene prevent neuronal growth, maturation and survival, essential for proper functioning of frontal cortical and subcortical circuits. However, more clinical evidence is required to confer the association of this particular variant rs8073224 with Attention-deficit hyperactivity disorder. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

4.5

DANN

Benign

0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over