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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;