rs4984814

Positions:

• chr16-1335649-A-C
• chr16-1335649-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199097.2(BAIAP3):​c.-11+1900A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,100 control chromosomes in the GnomAD database, including 14,120 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (14120 hom., cov: 34)
• Consequence: BAIAP3 NM_001199097.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAIAP3	NM_001199097.2	c.-11+1900A>C		intron_variant		ENST00000426824.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAIAP3	ENST00000426824.8	c.-11+1900A>C		intron_variant		2	NM_001199097.2	P1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63304 AN: 151984 Hom.: 14089 Cov.: 34

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.417 AC: 63381 AN: 152100 Hom.: 14120 Cov.: 34 AF XY: 0.420 AC XY: 31222 AN XY: 74360

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.423

Alfa AF: 0.436 Hom.: 3263

Bravo AF: 0.411

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs4984814; hg19: chr16-1385650; COSMIC: COSV60978727; COSMIC: COSV60978727;