rs1342913

Positions:

• chr1-190151895-G-A
• chr1-190151895-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP3	NM_199051.3	c.1184+8773C>T		intron_variant		ENST00000367462.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP3	ENST00000367462.5	c.1184+8773C>T		intron_variant		1	NM_199051.3	P1

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.575

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs1342913; hg19: chr1-190121025; COSMIC: COSV66517572;