rs10848167

Variant names:

• chr12-130639078-C-G
• rs10848167
• NM_001393629.1:c.-351-10622G>C

Variant summary

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

The NM_001393629.1(RIMBP2):​c.-351-10622G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 151,990 control chromosomes in the GnomAD database, including 32,637 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 0.65 (32637 hom., cov: 32)
• Consequence: RIMBP2 NM_001393629.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 5 publications found

Genes affected

RIMBP2 (HGNC:30339): (RIMS binding protein 2) Predicted to be involved in neuromuscular synaptic transmission. Predicted to be located in plasma membrane and synapse. Predicted to be active in presynaptic active zone cytoplasmic component. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RIMBP2	NM_001393629.1	c.-351-10622G>C		intron_variant	Intron 1 of 22	ENST00000690449.1	NP_001380558.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RIMBP2	ENST00000690449.1	c.-351-10622G>C		intron_variant	Intron 1 of 22		NM_001393629.1	ENSP00000509157.1

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99158 AN: 151872 Hom.: 32611 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.653 AC: 99231 AN: 151990 Hom.: 32637 Cov.: 32 AF XY: 0.661 AC XY: 49142 AN XY: 74302

African (AFR) AF: 0.557 AC: 23075 AN: 41438

American (AMR) AF: 0.731 AC: 11172 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3423 AN: 5154

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4824

European-Finnish (FIN) AF: 0.780 AC: 8236 AN: 10558

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45741 AN: 67950

Other (OTH) AF: 0.678 AC: 1430 AN: 2108

Alfa AF: 0.650 Hom.: 4000

Bravo AF: 0.644

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.84
PhyloP100		-0.097
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10848167; hg19: chr12-131123623;