Genetic Variant BAIAP3:p.Leu18Pro (chr16-1334714-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_003933.5(BAIAP3):c.53T>C(p.Leu18Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,556,848 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 3 hom., cov: 33)

Exomes 𝑓: 0.00096 ( 6 hom. )

Consequence

BAIAP3
NM_003933.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.44

Publications

4 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004722953).

BP6

Variant 16-1334714-T-C is Benign according to our data. Variant chr16-1334714-T-C is described in ClinVar as Benign. ClinVar VariationId is 3257643.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003933.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BAIAP3	NM_001199097.2	MANE Select	c.-11+965T>C		intron	N/A	NP_001186026.1	O94812-6
BAIAP3	NM_003933.5		c.53T>C	p.Leu18Pro	missense	Exon 1 of 34	NP_003924.2
BAIAP3	NM_001286464.2		c.-11+965T>C		intron	N/A	NP_001273393.2	O94812-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BAIAP3	ENST00000324385.9	TSL:1	c.53T>C	p.Leu18Pro	missense	Exon 1 of 34	ENSP00000324510.5	O94812-1
BAIAP3	ENST00000426824.8	TSL:2 MANE Select	c.-11+965T>C		intron	N/A	ENSP00000407242.4	O94812-6
BAIAP3	ENST00000397488.6	TSL:1	c.-11+965T>C		intron	N/A	ENSP00000380625.2	O94812-2

Frequencies

GnomAD3 genomes

AF:

0.00144

AC:

219

AN:

152016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000725

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00895

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00168

Gnomad OTH

AF:

0.00191

GnomAD2 exomes

AF:

0.00127

AC:

207

AN:

163052

AF XY:

0.00119

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000117

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00882

Gnomad NFE exome

AF:

0.000975

Gnomad OTH exome

AF:

0.00112

GnomAD4 exome

AF:

0.000963

AC:

1353

AN:

1404714

Hom.:

Cov.:

AF XY:

0.000943

AC XY:

654

AN XY:

693608

show subpopulations

African (AFR)

AF:

0.0000940

AC:

AN:

31918

American (AMR)

AF:

0.0000272

AC:

AN:

36762

Ashkenazi Jewish (ASJ)

AF:

0.000554

AC:

AN:

25252

East Asian (EAS)

AF:

0.00

AC:

AN:

36262

South Asian (SAS)

AF:

0.00

AC:

AN:

79644

European-Finnish (FIN)

AF:

0.0107

AC:

515

AN:

48286

Middle Eastern (MID)

AF:

0.000179

AC:

AN:

5582

European-Non Finnish (NFE)

AF:

0.000715

AC:

774

AN:

1082800

Other (OTH)

AF:

0.000773

AC:

AN:

58208

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

169

253

338

422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00144

AC:

219

AN:

152134

Hom.:

Cov.:

AF XY:

0.00161

AC XY:

120

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0000723

AC:

AN:

41510

American (AMR)

AF:

0.000131

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5148

South Asian (SAS)

AF:

0.00

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.00895

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00168

AC:

114

AN:

67964

Other (OTH)

AF:

0.00189

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00130

Hom.:

Bravo

AF:

0.000450

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000717

AC:

ExAC

AF:

0.000704

AC:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.45

CADD

Benign

1.3

(source)

DANN

Benign

0.76

DEOGEN2

Benign

0.011

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.31

MetaRNN

Benign

0.0047

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.55

PhyloP100

-2.4

PrimateAI

Uncertain

0.54

PROVEAN

Benign

0.21

REVEL

Benign

0.13

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.62

Vest4

0.16

MVP

0.49

MPC

0.29

ClinPred

0.036

GERP RS

-3.0

PromoterAI

0.048

Neutral

(source)

Varity_R

0.11

gMVP

0.37

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over