rs1156813

chr8-104234890-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001348484.3(RIMS2):c.4109-10026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,076 control chromosomes in the GnomAD database, including 2,468 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 0.16 (2468 hom., cov: 32)
• Consequence: RIMS2 NM_001348484.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274

Genes affected

RIMS2 (HGNC:17283): (regulating synaptic membrane exocytosis 2) The protein encoded by this gene is a presynaptic protein that interacts with RAB3, a protein important for normal neurotransmitter release. The encoded protein can also bind several other synaptic proteins, including UNC-13 homolog B, ELKS/Rab6-interacting/CAST family member 1, and synaptotagmin 1. This protein is involved in synaptic membrane exocytosis. Polymorphisms in this gene have been associated with degenerative lumbar scoliosis. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RIMS2	NM_001348484.3	c.4109-10026C>T		intron_variant		ENST00000696799.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RIMS2	ENST00000696799.1	c.4109-10026C>T		intron_variant			NM_001348484.3	A1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24155 AN: 151958 Hom.: 2468 Cov.: 32

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.159 AC: 24159 AN: 152076 Hom.: 2468 Cov.: 32 AF XY: 0.155 AC XY: 11561 AN XY: 74348

Gnomad4 AFR AF: 0.0509

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0918

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.162

Alfa AF: 0.191 Hom.: 377

Bravo AF: 0.147

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.77

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: rs1156813; hg19: chr8-105247118;