rs11057970

Positions:

• chr12-125002204-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRI3BP	NM_080626.6	c.213+8201C>T		intron_variant		ENST00000341446.9	NP_542193.3
BRI3BP	XM_011537940.3	c.213+8201C>T		intron_variant			XP_011536242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRI3BP	ENST00000341446.9	c.213+8201C>T		intron_variant		1	NM_080626.6	ENSP00000340761	P1
BRI3BP	ENST00000671775.2	c.213+8201C>T		intron_variant				ENSP00000500775
BRI3BP	ENST00000672415.1	c.213+8201C>T		intron_variant				ENSP00000500359	P1

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

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0503

Gnomad4 SAS AF: 0.00850

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0624

Gnomad4 OTH AF: 0.0761

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.68

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

LitVar

Other links and lift over

dbSNP: rs11057970; hg19: chr12-125486750;