Variant 17-81099993-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001144888.2(BAIAP2):c.555C>T(p.Thr185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,613,386 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 8 hom., cov: 33)

Exomes 𝑓: 0.0044 ( 69 hom. )

Consequence

BAIAP2
NM_001144888.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.69

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 17-81099993-C-T is Benign according to our data. Variant chr17-81099993-C-T is described in ClinVar as [Benign]. Clinvar id is 778754.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-6.69 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00344 (524/152320) while in subpopulation SAS AF= 0.0391 (189/4828). AF 95% confidence interval is 0.0346. There are 8 homozygotes in gnomad4. There are 283 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAIAP2	NM_001144888.2 linkuse as main transcript	c.555C>T	p.Thr185=	synonymous_variant	7/14	ENST00000428708.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAIAP2	ENST00000428708.7 linkuse as main transcript	c.555C>T	p.Thr185=	synonymous_variant	7/14	1	NM_001144888.2	A1	Q9UQB8-2

Frequencies

GnomAD3 genomes

AF:

0.00344

AC:

524

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00242

Gnomad ASJ

AF:

0.0127

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0389

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00298

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00682

AC:

1712

AN:

250862

Hom.:

AF XY:

0.00811

AC XY:

1101

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.000555

Gnomad AMR exome

AF:

0.00261

Gnomad ASJ exome

AF:

0.00914

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0330

Gnomad FIN exome

AF:

0.00143

Gnomad NFE exome

AF:

0.00382

Gnomad OTH exome

AF:

0.00784

GnomAD4 exome

AF:

0.00443

AC:

6466

AN:

1461066

Hom.:

Cov.:

AF XY:

0.00536

AC XY:

3894

AN XY:

726830

show subpopulations

Gnomad4 AFR exome

AF:

0.000448

Gnomad4 AMR exome

AF:

0.00255

Gnomad4 ASJ exome

AF:

0.0105

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0320

Gnomad4 FIN exome

AF:

0.00163

Gnomad4 NFE exome

AF:

0.00248

Gnomad4 OTH exome

AF:

0.00590

GnomAD4 genome

AF:

0.00344

AC:

524

AN:

152320

Hom.:

Cov.:

AF XY:

0.00380

AC XY:

283

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.00242

Gnomad4 ASJ

AF:

0.0127

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.0391

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00298

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00288

Hom.:

Bravo

AF:

0.00238

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.00453

EpiControl

AF:

0.00433

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.15

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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