rs1442569

chr1-190353597-C-Achr1-190353597-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199051.3(BRINP3):c.237-71847G>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 151,858 control chromosomes in the GnomAD database, including 2,078 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 (2078 hom., cov: 32)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRINP3	NM_199051.3	c.237-71847G>T		intron_variant		ENST00000367462.5
LOC105371658	XR_001738344.2	n.152-8466C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRINP3	ENST00000367462.5	c.237-71847G>T		intron_variant		1	NM_199051.3	P1
	ENST00000452178.1	n.395-8466C>A		intron_variant, non_coding_transcript_variant		5
BRINP3	ENST00000631494.1	c.237-71847G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24217 AN: 151740 Hom.: 2075 Cov.: 32

Gnomad AFR AF: 0.0951

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.160 AC: 24227 AN: 151858 Hom.: 2078 Cov.: 32 AF XY: 0.162 AC XY: 12047 AN XY: 74194

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.130

Alfa AF: 0.133 Hom.: 478

Bravo AF: 0.145

Asia WGS AF: 0.163 AC: 566 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.34
Dann	Benign	0.21

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: rs1442569; hg19: chr1-190322727;