chr1-190318583-G-A

Variant names:

• chr1-190318583-G-A
• rs655598
• NM_199051.3:c.237-36833C>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.237-36833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,758 control chromosomes in the GnomAD database, including 24,192 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 0.56 (24192 hom., cov: 31)
• Consequence: BRINP3 NM_199051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.237-36833C>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.237-36833C>T		intron_variant	Intron 2 of 7	1	NM_199051.3	ENSP00000356432.3
BRINP3	ENST00000631494.1	c.237-36833C>T		intron_variant	Intron 2 of 3	4		ENSP00000487601.1
ENSG00000225811	ENST00000452178.1	n.231+15792G>A		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85163 AN: 151638 Hom.: 24158 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.562 AC: 85247 AN: 151758 Hom.: 24192 Cov.: 31 AF XY: 0.561 AC XY: 41599 AN XY: 74150

African (AFR) AF: 0.506 AC: 20930 AN: 41356

American (AMR) AF: 0.683 AC: 10389 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3228 AN: 5128

South Asian (SAS) AF: 0.652 AC: 3143 AN: 4822

European-Finnish (FIN) AF: 0.463 AC: 4878 AN: 10546

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38548 AN: 67910

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.576 Hom.: 77546

Bravo AF: 0.576

Asia WGS AF: 0.650 AC: 2261 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.16
PhyloP100		-0.076
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: rs655598; hg19: chr1-190287713;