rs1333322

chr1-190155607-A-C

Variant summary

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

The NM_199051.3(BRINP3):c.1184+5061T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,878 control chromosomes in the GnomAD database, including 2,023 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 0.13 (2023 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.595

Genes affected

BRINP3 (HGNC:22393): (BMP/retinoic acid inducible neural specific 3) This gene is overexpressed in pituitary tumors but is underexpressed in tongue squamous cell carcinomas, ulcerative colitis, and peri-implantitis. Polymorphisms that increase expression of this gene have been shown to increase vascular inflammation, and an association of this gene with myocardial infarction has been demonstrated. Finally, hypermethylation of this gene may find usefulness as a biomarker for gastric cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP3	NM_199051.3	c.1184+5061T>G		intron_variant		ENST00000367462.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP3	ENST00000367462.5	c.1184+5061T>G		intron_variant		1	NM_199051.3	P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20374 AN: 151760 Hom.: 2014 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0552

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.134 AC: 20405 AN: 151878 Hom.: 2023 Cov.: 32 AF XY: 0.136 AC XY: 10133 AN XY: 74242

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.0552

Gnomad4 OTH AF: 0.141

Alfa AF: 0.119 Hom.: 253

Bravo AF: 0.150

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	4.9
Dann	Benign	0.53

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: rs1333322; hg19: chr1-190124737;