1-190139751-C-T

Variant names:

• chr1-190139751-C-T
• rs2419370
• NM_199051.3:c.1184+20917G>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.1184+20917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,880 control chromosomes in the GnomAD database, including 28,920 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 0.60 (28920 hom., cov: 31)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.1184+20917G>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.1184+20917G>A		intron_variant	Intron 7 of 7	1	NM_199051.3	ENSP00000356432.3

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90524 AN: 151762 Hom.: 28841 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.597 AC: 90668 AN: 151880 Hom.: 28920 Cov.: 31 AF XY: 0.592 AC XY: 43897 AN XY: 74184

African (AFR) AF: 0.841 AC: 34875 AN: 41484

American (AMR) AF: 0.590 AC: 9002 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1963 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2774 AN: 5120

South Asian (SAS) AF: 0.550 AC: 2653 AN: 4828

European-Finnish (FIN) AF: 0.416 AC: 4379 AN: 10522

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33084 AN: 67902

Other (OTH) AF: 0.582 AC: 1225 AN: 2106

Alfa AF: 0.508 Hom.: 37086

Bravo AF: 0.622

Asia WGS AF: 0.578 AC: 2010 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.30
PhyloP100		-0.62
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: rs2419370; hg19: chr1-190108881;