16-1339164-G-C

Variant names:

• chr16-1339164-G-C
• rs1192243058
• ENST00000397488.6:c.271G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001199097.2(BAIAP3):​c.220G>C​(p.Val74Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000424 in 1,414,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 0.0000042 (0 hom.)
• Consequence: BAIAP3 NM_001199097.2 missense, splice_region
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.426
• Publications: 0 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.220G>C	p.Val74Leu	missense splice_region	Exon 4 of 34	NP_001186026.1	O94812-6
	BAIAP3	NM_001286464.2		c.271G>C	p.Val91Leu	missense	Exon 4 of 34	NP_001273393.2	O94812-2
	BAIAP3	NM_003933.5		c.325G>C	p.Val109Leu	missense splice_region	Exon 4 of 34	NP_003924.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAIAP3	ENST00000397488.6	TSL:1	c.271G>C	p.Val91Leu	missense	Exon 4 of 34	ENSP00000380625.2	O94812-2
	BAIAP3	ENST00000426824.8	TSL:2 MANE Select	c.220G>C	p.Val74Leu	missense splice_region	Exon 4 of 34	ENSP00000407242.4	O94812-6
	BAIAP3	ENST00000324385.9	TSL:1	c.325G>C	p.Val109Leu	missense splice_region	Exon 4 of 34	ENSP00000324510.5	O94812-1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD2 exomes AF: 0.0000292 AC: 5 AN: 171312 AF XY: 0.0000432

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000393

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000424 AC: 6 AN: 1414762 Hom.: 0 Cov.: 36 AF XY: 0.00000572 AC XY: 4 AN XY: 699706

African (AFR) AF: 0.00 AC: 0 AN: 32496

American (AMR) AF: 0.00 AC: 0 AN: 36750

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25328

East Asian (EAS) AF: 0.000161 AC: 6 AN: 37188

South Asian (SAS) AF: 0.00 AC: 0 AN: 81304

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47904

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5706

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1089346

Other (OTH) AF: 0.00 AC: 0 AN: 58740

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000227

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	0.15
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	14
DANN	Uncertain	0.99
DEOGEN2	Benign	0.020	T
Eigen	Benign	-0.077
Eigen_PC	Benign	-0.045
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Benign	0.83	T
M_CAP	Uncertain	0.23	D
MetaRNN	Benign	0.28	T
MetaSVM	Benign	-0.57	T
MutationAssessor	Benign	2.0	M
PhyloP100		0.43
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-1.2	N
REVEL	Uncertain	0.30
Sift	Benign	0.043	D
Sift4G	Benign	0.68	T
Polyphen		0.69	P
Vest4		0.37
MutPred		0.44		Gain of catalytic residue at V109 (P = 0.0337)
MVP		0.75
MPC		0.46
ClinPred		0.078	T
GERP RS		4.1
Varity_R		0.13
gMVP		0.16
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.35		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.35		Position offset: 0

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

Other links and lift over

dbSNP: rs1192243058; hg19: chr16-1389165;