16-11267345-A-G

Variant names:

• chr16-11267345-A-G
• rs243323
• ENST00000572173.1:c.-516+17567A>G

Variant summary

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

The ENST00000572173.1(RMI2):​c.-516+17567A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,108 control chromosomes in the GnomAD database, including 11,713 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 0.38 (11713 hom., cov: 33)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 34 publications found

Genes affected

RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

LOC105371082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572173.1. You can select a different transcript below to see updated ACMG assignments.

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
	RMI2	ENST00000572173.1	TSL:1	c.-516+17567A>G		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.160+17567A>G		intron	N/A
	RMI2	ENST00000649869.1		n.152+17567A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56971 AN: 151990 Hom.: 11685 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.375 AC: 57056 AN: 152108 Hom.: 11713 Cov.: 33 AF XY: 0.385 AC XY: 28597 AN XY: 74348

African (AFR) AF: 0.409 AC: 16969 AN: 41482

American (AMR) AF: 0.496 AC: 7589 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1217 AN: 3470

East Asian (EAS) AF: 0.731 AC: 3795 AN: 5188

South Asian (SAS) AF: 0.590 AC: 2847 AN: 4824

European-Finnish (FIN) AF: 0.315 AC: 3332 AN: 10574

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20240 AN: 67966

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.330 Hom.: 29374

Bravo AF: 0.394

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	7.8
DANN	Benign	0.91
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs243323;

hg19: chr16-11361202;