rs922873

Variant names:

• chr12-125042381-G-A
• rs922873
• XM_011537940.3:c.317-8581G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011537940.3(BRI3BP):​c.317-8581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,060 control chromosomes in the GnomAD database, including 46,306 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 0.78 (46306 hom., cov: 32)
• Consequence: BRI3BP XM_011537940.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 2 publications found

Genes affected

BRI3BP (HGNC:14251): (BRI3 binding protein) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRI3BP	XM_011537940.3	c.317-8581G>A		intron_variant	Intron 2 of 2		XP_011536242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118423 AN: 151948 Hom.: 46244 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.780 AC: 118544 AN: 152060 Hom.: 46306 Cov.: 32 AF XY: 0.788 AC XY: 58566 AN XY: 74324

African (AFR) AF: 0.745 AC: 30903 AN: 41460

American (AMR) AF: 0.805 AC: 12272 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3472

East Asian (EAS) AF: 0.812 AC: 4207 AN: 5184

South Asian (SAS) AF: 0.850 AC: 4089 AN: 4808

European-Finnish (FIN) AF: 0.897 AC: 9493 AN: 10582

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.771 AC: 52444 AN: 67992

Other (OTH) AF: 0.768 AC: 1621 AN: 2112

Alfa AF: 0.770 Hom.: 67994

Bravo AF: 0.767

Asia WGS AF: 0.828 AC: 2881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.35
PhyloP100		-0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs922873; hg19: chr12-125526927;