rs12142564

Variant names:

• chr1-190102873-C-T
• rs12142564
• NM_199051.3:c.1185-3739G>A

Variant summary

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

The NM_199051.3(BRINP3):​c.1185-3739G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 151,854 control chromosomes in the GnomAD database, including 855 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 0.10 (855 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.1185-3739G>A		intron_variant	Intron 7 of 7	ENST00000367462.5	NP_950252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP3	ENST00000367462.5	c.1185-3739G>A		intron_variant	Intron 7 of 7	1	NM_199051.3	ENSP00000356432.3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15192 AN: 151736 Hom.: 850 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0928

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.100 AC: 15213 AN: 151854 Hom.: 855 Cov.: 32 AF XY: 0.102 AC XY: 7534 AN XY: 74226

African (AFR) AF: 0.0756 AC: 3138 AN: 41492

American (AMR) AF: 0.0867 AC: 1323 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 490 AN: 3454

East Asian (EAS) AF: 0.0928 AC: 479 AN: 5162

South Asian (SAS) AF: 0.0902 AC: 433 AN: 4798

European-Finnish (FIN) AF: 0.142 AC: 1497 AN: 10562

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7454 AN: 67822

Other (OTH) AF: 0.115 AC: 243 AN: 2110

Alfa AF: 0.101 Hom.: 315

Bravo AF: 0.0949

Asia WGS AF: 0.107 AC: 373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-0.75
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: rs12142564; hg19: chr1-190072003;