rs1891586

chr1-190194864-T-G

Variant summary

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

The NM_199051.3(BRINP3):c.961+31218A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,984 control chromosomes in the GnomAD database, including 3,653 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 0.21 (3653 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

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=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP3	NM_199051.3	c.961+31218A>C		intron_variant		ENST00000367462.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP3	ENST00000367462.5	c.961+31218A>C		intron_variant		1	NM_199051.3	P1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31822 AN: 151866 Hom.: 3650 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.209 AC: 31831 AN: 151984 Hom.: 3653 Cov.: 32 AF XY: 0.209 AC XY: 15532 AN XY: 74242

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.190

Alfa AF: 0.226 Hom.: 527

Bravo AF: 0.194

Asia WGS AF: 0.170 AC: 589 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	8.5
Dann	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1891586; hg19: chr1-190163994;