chr1-190151895-G-A

Variant names:

• chr1-190151895-G-A
• rs1342913
• NM_199051.3:c.1184+8773C>T

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+8773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,024 control chromosomes in the GnomAD database, including 29,387 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 0.61 (29387 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 6 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 = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199051.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRINP3	NM_199051.3	MANE Select	c.1184+8773C>T		intron	N/A	NP_950252.1
	BRINP3	NM_001317188.2		c.878+8773C>T		intron	N/A	NP_001304117.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRINP3	ENST00000367462.5	TSL:1 MANE Select	c.1184+8773C>T		intron	N/A	ENSP00000356432.3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92035 AN: 151906 Hom.: 29320 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.606 AC: 92169 AN: 152024 Hom.: 29387 Cov.: 32 AF XY: 0.606 AC XY: 45049 AN XY: 74302

African (AFR) AF: 0.830 AC: 34462 AN: 41524

American (AMR) AF: 0.510 AC: 7790 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3110 AN: 5156

South Asian (SAS) AF: 0.617 AC: 2971 AN: 4816

European-Finnish (FIN) AF: 0.555 AC: 5856 AN: 10544

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34141 AN: 67938

Other (OTH) AF: 0.575 AC: 1212 AN: 2106

Alfa AF: 0.557 Hom.: 3921

Bravo AF: 0.612

Asia WGS AF: 0.607 AC: 2106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.50
PhyloP100		0.091
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: rs1342913; hg19: chr1-190121025; COSMIC: COSV66517572;