rs423674

Variant names:

• chr16-11279548-G-T
• rs423674
• ENST00000572173.1:c.-515-15668G>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-515-15668G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,126 control chromosomes in the GnomAD database, including 2,537 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 0.18 (2537 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 17 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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.-515-15668G>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.160+29770G>T		intron	N/A
	RMI2	ENST00000649869.1		n.152+29770G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27302 AN: 152008 Hom.: 2527 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.180 AC: 27339 AN: 152126 Hom.: 2537 Cov.: 31 AF XY: 0.174 AC XY: 12924 AN XY: 74364

African (AFR) AF: 0.217 AC: 9021 AN: 41478

American (AMR) AF: 0.124 AC: 1890 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3464

East Asian (EAS) AF: 0.0476 AC: 246 AN: 5170

South Asian (SAS) AF: 0.126 AC: 606 AN: 4820

European-Finnish (FIN) AF: 0.149 AC: 1579 AN: 10592

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 12992 AN: 67988

Other (OTH) AF: 0.149 AC: 316 AN: 2116

Alfa AF: 0.184 Hom.: 4056

Bravo AF: 0.180

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.44
PhyloP100		-0.20
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: rs423674;

hg19: chr16-11373405;