16-1338671-C-T

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

4
15

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]

Genome browser will be placed here

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
BAIAP3NM_001199097.2 linkc.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
BAIAP3ENST00000426824.8 linkc.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.:
1
Cov.:
32
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.:
2
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.:
14
Cov.:
35
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.:
1
Cov.:
32
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.:
1
Bravo
AF:
0.00279
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.00156
AC:
6
ESP6500AA
AF:
0.000232
AC:
1
ESP6500EA
AF:
0.00473
AC:
40
ExAC
AF:
0.00253
AC:
301
Asia WGS
AF:
0.00231
AC:
8
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
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.022
.;.;.;.;T;.;.
Eigen
Benign
-0.42
Eigen_PC
Benign
-0.56
FATHMM_MKL
Benign
0.17
N
LIST_S2
Benign
0.72
T;.;T;T;T;T;T
M_CAP
Uncertain
0.13
D
MetaRNN
Benign
0.0095
T;T;T;T;T;T;T
MetaSVM
Benign
-0.78
T
MutationAssessor
Benign
1.9
.;.;.;.;M;.;.
PrimateAI
Benign
0.45
T
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
T
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.

Other links and lift over

dbSNP: rs116106398; hg19: chr16-1388672; COSMIC: COSV100181323; COSMIC: COSV100181323; API