rs12922090

Variant names:

• chr16-11321260-C-T
• rs12922090
• ENST00000572173.1:c.106+4376C>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.106+4376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,220 control chromosomes in the GnomAD database, including 1,200 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 0.11 (1200 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 15 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 = 0.164 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.106+4376C>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000649869.1		n.153-58562C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17029 AN: 152102 Hom.: 1199 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.112 AC: 17028 AN: 152220 Hom.: 1200 Cov.: 32 AF XY: 0.109 AC XY: 8127 AN XY: 74414

African (AFR) AF: 0.0299 AC: 1242 AN: 41558

American (AMR) AF: 0.0936 AC: 1432 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 441 AN: 3470

East Asian (EAS) AF: 0.0432 AC: 224 AN: 5180

South Asian (SAS) AF: 0.101 AC: 489 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11304 AN: 67988

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.133 Hom.: 263

Bravo AF: 0.107

Asia WGS AF: 0.0650 AC: 228 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	2.2
DANN	Benign	0.72
PhyloP100		-0.13
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: rs12922090;

hg19: chr16-11415117;