rs243315

Variant names:

• chr16-11291154-C-T
• rs243315
• ENST00000572173.1:c.-515-4062C>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-515-4062C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,086 control chromosomes in the GnomAD database, including 1,553 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 0.13 (1553 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 10 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]

ENSG00000287429 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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.-515-4062C>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.161-25298C>T		intron	N/A
	RMI2	ENST00000649869.1		n.152+41376C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19319 AN: 151968 Hom.: 1552 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.127 AC: 19320 AN: 152086 Hom.: 1553 Cov.: 32 AF XY: 0.123 AC XY: 9136 AN XY: 74340

African (AFR) AF: 0.0341 AC: 1414 AN: 41512

American (AMR) AF: 0.101 AC: 1548 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3472

East Asian (EAS) AF: 0.0464 AC: 240 AN: 5172

South Asian (SAS) AF: 0.117 AC: 564 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1578 AN: 10578

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13053 AN: 67950

Other (OTH) AF: 0.112 AC: 236 AN: 2112

Alfa AF: 0.150 Hom.: 338

Bravo AF: 0.121

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.29
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: rs243315;

hg19: chr16-11385011;