chr16-11302058-G-A

Variant names:

• chr16-11302058-G-A
• rs12599908
• ENST00000572173.1:c.-437+6764G>A

Variant summary

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

The ENST00000572173.1(RMI2):​c.-437+6764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,090 control chromosomes in the GnomAD database, including 1,888 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 0.15 (1888 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 7 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=-0.93).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000572173.1	TSL:1	c.-437+6764G>A		intron	N/A	ENSP00000461206.1
	RMI2	ENST00000573910.1	TSL:3	n.161-14394G>A		intron	N/A
	RMI2	ENST00000649869.1		n.152+52280G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23488 AN: 151972 Hom.: 1887 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.155 AC: 23505 AN: 152090 Hom.: 1888 Cov.: 32 AF XY: 0.150 AC XY: 11119 AN XY: 74336

African (AFR) AF: 0.132 AC: 5482 AN: 41474

American (AMR) AF: 0.108 AC: 1644 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3466

East Asian (EAS) AF: 0.0445 AC: 231 AN: 5186

South Asian (SAS) AF: 0.116 AC: 558 AN: 4820

European-Finnish (FIN) AF: 0.149 AC: 1579 AN: 10562

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13052 AN: 68000

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.100 Hom.: 142

Bravo AF: 0.152

Asia WGS AF: 0.0800 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.35
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12599908; hg19: chr16-11395915;