rs12076854

Variant names:

• chr1-190165941-T-A
• rs12076854
• NM_199051.3:c.962-5051A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-190165941-T-A
• chr1-190165941-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199051.3(BRINP3):​c.962-5051A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,032 control chromosomes in the GnomAD database, including 3,150 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 0.16 (3150 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.962-5051A>T		intron_variant	Intron 6 of 7	ENST00000367462.5	NP_950252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP3	ENST00000367462.5	c.962-5051A>T		intron_variant	Intron 6 of 7	1	NM_199051.3	ENSP00000356432.3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24235 AN: 151912 Hom.: 3126 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.160 AC: 24308 AN: 152032 Hom.: 3150 Cov.: 32 AF XY: 0.162 AC XY: 12030 AN XY: 74330

African (AFR) AF: 0.339 AC: 14057 AN: 41426

American (AMR) AF: 0.180 AC: 2745 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3466

East Asian (EAS) AF: 0.244 AC: 1261 AN: 5158

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4818

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10606

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0552 AC: 3749 AN: 67972

Other (OTH) AF: 0.168 AC: 355 AN: 2108

Alfa AF: 0.0410 Hom.: 64

Bravo AF: 0.179

Asia WGS AF: 0.252 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12076854; hg19: chr1-190135071;