rs1053081

Variant names:

• chr1-190097855-A-G
• rs1053081
• NM_199051.3:c.*163T>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_199051.3(BRINP3):​c.*163T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00973 in 742,570 control chromosomes in the GnomAD database, including 51 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 0.0080 (12 hom., cov: 32)
  • Exomes 𝑓: 0.010 (39 hom.)
• Consequence: BRINP3 NM_199051.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.51
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BS2: High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRINP3	NM_199051.3	c.*163T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000367462.5	NP_950252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRINP3	ENST00000367462.5	c.*163T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_199051.3	ENSP00000356432.3

Frequencies

GnomAD3 genomes AF: 0.00798 AC: 1215 AN: 152176 Hom.: 12 Cov.: 32

Gnomad AFR AF: 0.00217

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00475

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0120

GnomAD4 exome AF: 0.0102 AC: 6009 AN: 590276 Hom.: 39 Cov.: 8 AF XY: 0.0103 AC XY: 3135 AN XY: 304920

African (AFR) AF: 0.00229 AC: 35 AN: 15262

American (AMR) AF: 0.00775 AC: 151 AN: 19482

Ashkenazi Jewish (ASJ) AF: 0.00763 AC: 112 AN: 14676

East Asian (EAS) AF: 0.00 AC: 0 AN: 32838

South Asian (SAS) AF: 0.00494 AC: 229 AN: 46322

European-Finnish (FIN) AF: 0.00322 AC: 105 AN: 32628

Middle Eastern (MID) AF: 0.0159 AC: 36 AN: 2262

European-Non Finnish (NFE) AF: 0.0127 AC: 5046 AN: 396250

Other (OTH) AF: 0.00965 AC: 295 AN: 30556

GnomAD4 genome AF: 0.00798 AC: 1215 AN: 152294 Hom.: 12 Cov.: 32 AF XY: 0.00765 AC XY: 570 AN XY: 74478

African (AFR) AF: 0.00217 AC: 90 AN: 41568

American (AMR) AF: 0.00981 AC: 150 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00476 AC: 23 AN: 4834

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 867 AN: 68008

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.00991 Hom.: 5

Bravo AF: 0.00777

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		3.5
Mutation Taster		=100/0	polymorphism

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: rs1053081; hg19: chr1-190066985;