rs367569

Variant names:

• chr16-11271643-C-T
• rs367569
• ENST00000572173.1:c.-516+21865C>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-516+21865C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,982 control chromosomes in the GnomAD database, including 7,907 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 0.31 (7907 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 31 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.383 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+21865C>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.160+21865C>T		intron	N/A
	RMI2	ENST00000649869.1		n.152+21865C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47738 AN: 151864 Hom.: 7881 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.315 AC: 47824 AN: 151982 Hom.: 7907 Cov.: 32 AF XY: 0.314 AC XY: 23364 AN XY: 74294

African (AFR) AF: 0.369 AC: 15281 AN: 41422

American (AMR) AF: 0.391 AC: 5976 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3466

East Asian (EAS) AF: 0.143 AC: 736 AN: 5164

South Asian (SAS) AF: 0.300 AC: 1446 AN: 4818

European-Finnish (FIN) AF: 0.291 AC: 3074 AN: 10576

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19240 AN: 67950

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.312 Hom.: 4597

Bravo AF: 0.330

Asia WGS AF: 0.269 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.017
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: rs367569;

hg19: chr16-11365500;