rs1442569

Variant names:

• chr1-190353597-C-A
• rs1442569
• NM_199051.3:c.237-71847G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-190353597-C-A
• chr1-190353597-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ENSG00000225811 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.237-71847G>T		intron_variant	Intron 2 of 7	ENST00000367462.5	NP_950252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP3	ENST00000367462.5	c.237-71847G>T		intron_variant	Intron 2 of 7	1	NM_199051.3	ENSP00000356432.3
BRINP3	ENST00000631494.1	c.237-71847G>T		intron_variant	Intron 2 of 3	4		ENSP00000487601.1
ENSG00000225811	ENST00000452178.1	n.395-8466C>A		intron_variant	Intron 4 of 4	5

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

African (AFR) AF: 0.0949 AC: 3935 AN: 41476

American (AMR) AF: 0.120 AC: 1819 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3464

East Asian (EAS) AF: 0.152 AC: 780 AN: 5140

South Asian (SAS) AF: 0.204 AC: 984 AN: 4816

European-Finnish (FIN) AF: 0.246 AC: 2606 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12937 AN: 67862

Other (OTH) AF: 0.130 AC: 274 AN: 2104

Alfa AF: 0.132 Hom.: 484

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
PhyloP100		-0.54
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: rs1442569; hg19: chr1-190322727;