chr16-1339173-C-T

Variant names:

• chr16-1339173-C-T
• rs762143694
• NM_001199097.2:c.229C>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_001199097.2(BAIAP3):​c.229C>T​(p.Arg77Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000402 in 1,565,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R77H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 34)
  • Exomes 𝑓: 0.000030 (0 hom.)
• Consequence: BAIAP3 NM_001199097.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.721
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.3122309).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001199097.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAIAP3	NM_001199097.2	MANE Select	c.229C>T	p.Arg77Cys	missense	Exon 4 of 34	NP_001186026.1	O94812-6
	BAIAP3	NM_003933.5		c.334C>T	p.Arg112Cys	missense	Exon 4 of 34	NP_003924.2
	BAIAP3	NM_001286464.2		c.280C>T	p.Arg94Cys	missense	Exon 4 of 34	NP_001273393.2	O94812-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAIAP3	ENST00000426824.8	TSL:2 MANE Select	c.229C>T	p.Arg77Cys	missense	Exon 4 of 34	ENSP00000407242.4	O94812-6
	BAIAP3	ENST00000324385.9	TSL:1	c.334C>T	p.Arg112Cys	missense	Exon 4 of 34	ENSP00000324510.5	O94812-1
	BAIAP3	ENST00000397488.6	TSL:1	c.280C>T	p.Arg94Cys	missense	Exon 4 of 34	ENSP00000380625.2	O94812-2

Frequencies

GnomAD3 genomes AF: 0.000125 AC: 19 AN: 152164 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.0000416 AC: 7 AN: 168356 AF XY: 0.0000439

Gnomad AFR exome AF: 0.000114

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000725

Gnomad OTH exome AF: 0.000218

GnomAD4 exome AF: 0.0000304 AC: 43 AN: 1413480 Hom.: 0 Cov.: 36 AF XY: 0.0000215 AC XY: 15 AN XY: 698972

African (AFR) AF: 0.000185 AC: 6 AN: 32450

American (AMR) AF: 0.00 AC: 0 AN: 36708

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25306

East Asian (EAS) AF: 0.00 AC: 0 AN: 37140

South Asian (SAS) AF: 0.00 AC: 0 AN: 81080

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47470

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5700

European-Non Finnish (NFE) AF: 0.0000312 AC: 34 AN: 1088984

Other (OTH) AF: 0.0000512 AC: 3 AN: 58642

GnomAD4 genome AF: 0.000131 AC: 20 AN: 152282 Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 8 AN XY: 74458

African (AFR) AF: 0.000265 AC: 11 AN: 41540

American (AMR) AF: 0.000131 AC: 2 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000882 AC: 6 AN: 68008

Other (OTH) AF: 0.000473 AC: 1 AN: 2116

Alfa AF: 0.000141 Hom.: 0

Bravo AF: 0.000147

ExAC AF: 0.00000864 AC: 1

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.013	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	15
DANN	Uncertain	1.0
DEOGEN2	Benign	0.18	T
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.45
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.84	T
M_CAP	Pathogenic	0.38	D
MetaRNN	Benign	0.31	T
MetaSVM	Uncertain	0.14	D
MutationAssessor	Benign	1.9	M
PhyloP100		-0.72
PrimateAI	Uncertain	0.70	T
PROVEAN	Uncertain	-3.5	D
REVEL	Benign	0.28
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0050	D
Polyphen		0.010	B
Vest4		0.34
MVP		0.79
MPC		0.45
ClinPred		0.35	T
GERP RS		4.1
Varity_R		0.25
gMVP		0.24
Mutation Taster		=92/8	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs762143694; hg19: chr16-1389174;