Genetic Variant BAIAP3:p.Thr41Met (chr16-1338671-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001199097.2(BAIAP3):c.122C>T(p.Thr41Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,582,006 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 14 hom. )

Consequence

BAIAP3
NM_001199097.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.169

Variant links:

Genes affected

BAIAP3 (HGNC:948): (BAI1 associated protein 3) This p53-target gene encodes a brain-specific angiogenesis inhibitor. The protein is a seven-span transmembrane protein and a member of the secretin receptor family. It interacts with the cytoplasmic region of brain-specific angiogenesis inhibitor 1. This protein also contains two C2 domains, which are often found in proteins involved in signal transduction or membrane trafficking. Its expression pattern and similarity to other proteins suggest that it may be involved in synaptic functions. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

BAIAP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00945434).

BP6

Variant 16-1338671-C-T is Benign according to our data. Variant chr16-1338671-C-T is described in ClinVar as [Benign]. Clinvar id is 2645890.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAIAP3	NM_001199097.2 link	c.122C>T	p.Thr41Met	missense_variant	Exon 2 of 34	ENST00000426824.8	NP_001186026.1	O94812-6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAIAP3	ENST00000426824.8 link	c.122C>T	p.Thr41Met	missense_variant	Exon 2 of 34	2	NM_001199097.2	ENSP00000407242.4		O94812-6

Frequencies

GnomAD3 genomes

AF:

0.00242

AC:

369

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000483

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.00235

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00340

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00287

AC:

557

AN:

193810

Hom.:

AF XY:

0.00285

AC XY:

301

AN XY:

105436

show subpopulations

Gnomad AFR exome

AF:

0.000827

Gnomad AMR exome

AF:

0.00223

Gnomad ASJ exome

AF:

0.00971

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00222

Gnomad FIN exome

AF:

0.000183

Gnomad NFE exome

AF:

0.00367

Gnomad OTH exome

AF:

0.00612

GnomAD4 exome

AF:

0.00270

AC:

3854

AN:

1429706

Hom.:

Cov.:

AF XY:

0.00277

AC XY:

1964

AN XY:

708826

show subpopulations

Gnomad4 AFR exome

AF:

0.000850

Gnomad4 AMR exome

AF:

0.00275

Gnomad4 ASJ exome

AF:

0.00940

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00220

Gnomad4 FIN exome

AF:

0.000388

Gnomad4 NFE exome

AF:

0.00273

Gnomad4 OTH exome

AF:

0.00349

GnomAD4 genome

AF:

0.00244

AC:

371

AN:

152300

Hom.:

Cov.:

AF XY:

0.00224

AC XY:

167

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.000481

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00340

Gnomad4 OTH

AF:

0.00614

Alfa

AF:

0.00400

Hom.:

Bravo

AF:

0.00279

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.00156

AC:

ESP6500AA

AF:

0.000232

AC:

ESP6500EA

AF:

0.00473

AC:

ExAC

AF:

0.00253

AC:

301

Asia WGS

AF:

0.00231

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BAIAP3: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.083

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.022

.;.;.;.;T;.;.

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.56

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.72

T;.;T;T;T;T;T

M_CAP

Uncertain

0.13

MetaRNN

Benign

0.0095

T;T;T;T;T;T;T

MetaSVM

Benign

-0.78

MutationAssessor

Benign

1.9

.;.;.;.;M;.;.

PrimateAI

Benign

0.45

PROVEAN

Benign

-1.7

N;N;N;N;N;.;N

REVEL

Benign

0.16

Sift

Uncertain

0.0030

D;D;D;D;D;.;D

Sift4G

Uncertain

0.012

D;D;D;D;D;D;D

Polyphen

0.91

.;.;.;.;P;.;.

Vest4

0.14

MVP

0.81

MPC

0.37

ClinPred

0.017

GERP RS

2.4

Varity_R

0.035

gMVP

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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