dbSNP rs12732361: BRINP3:c.-279C>G (chr1-190477676-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_199051.3(BRINP3):c.-279C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,200 control chromosomes in the GnomAD database, including 2,816 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 0.19 ( 2815 hom., cov: 30)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

BRINP3
NM_199051.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0900

Publications

2 publications found

Variant links:

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]

BRINP3 links:

BRINP3-DT (HGNC:50577): (BRINP3 divergent transcript)

BRINP3-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3 link	c.-279C>G		5_prime_UTR_variant	Exon 1 of 8	ENST00000367462.5	NP_950252.1	Q76B58-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP3	ENST00000367462.5 link	c.-279C>G		5_prime_UTR_variant	Exon 1 of 8	1	NM_199051.3	ENSP00000356432.3		Q76B58-1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28700

AN:

151032

Hom.:

2806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.204

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.222

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

Cov.:

AF XY:

0.100

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.130

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.555

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.190

AC:

28736

AN:

151144

Hom.:

2815

Cov.:

AF XY:

0.191

AC XY:

14126

AN XY:

73824

show subpopulations

African (AFR)

AF:

0.162

AC:

6620

AN:

40770

American (AMR)

AF:

0.183

AC:

2793

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.204

AC:

708

AN:

3466

East Asian (EAS)

AF:

0.187

AC:

961

AN:

5140

South Asian (SAS)

AF:

0.224

AC:

1067

AN:

4758

European-Finnish (FIN)

AF:

0.225

AC:

2372

AN:

10538

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.199

AC:

13532

AN:

67920

Other (OTH)

AF:

0.164

AC:

345

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1159

2317

3476

4634

5793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.190

Hom.:

345

Bravo

AF:

0.184

Asia WGS

AF:

0.193

AC:

670

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.7

(source)

DANN

Benign

0.25

PhyloP100

-0.090

PromoterAI

-0.088

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs12732361

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over