chr12-125002204-C-T

Variant names:

• chr12-125002204-C-T
• rs11057970
• NM_080626.6:c.213+8201C>T

Variant summary

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

The NM_080626.6(BRI3BP):​c.213+8201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0546 in 152,166 control chromosomes in the GnomAD database, including 396 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 0.055 (396 hom., cov: 33)
• Consequence: BRI3BP NM_080626.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080626.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRI3BP	NM_080626.6	MANE Select	c.213+8201C>T		intron	N/A	NP_542193.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRI3BP	ENST00000341446.9	TSL:1 MANE Select	c.213+8201C>T		intron	N/A	ENSP00000340761.7
	BRI3BP	ENST00000671775.2		c.213+8201C>T		intron	N/A	ENSP00000500775.2
	BRI3BP	ENST00000672415.1		c.213+8201C>T		intron	N/A	ENSP00000500359.1

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8304 AN: 152048 Hom.: 394 Cov.: 33

Gnomad AFR AF: 0.0130

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.00870

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0774

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

GnomAD4 genome AF: 0.0546 AC: 8302 AN: 152166 Hom.: 396 Cov.: 33 AF XY: 0.0542 AC XY: 4031 AN XY: 74398

African (AFR) AF: 0.0129 AC: 536 AN: 41510

American (AMR) AF: 0.141 AC: 2160 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3466

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5174

South Asian (SAS) AF: 0.00850 AC: 41 AN: 4824

European-Finnish (FIN) AF: 0.0342 AC: 363 AN: 10600

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0624 AC: 4244 AN: 68004

Other (OTH) AF: 0.0761 AC: 161 AN: 2116

Alfa AF: 0.0746 Hom.: 104

Bravo AF: 0.0632

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.68
PhyloP100		0.019
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: rs11057970; hg19: chr12-125486750;