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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.179-58562C>T		intron_variant	Intron 1 of 2
LOC105371082	XR_933073.3	n.809+4376C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.106+4376C>T		intron_variant	Intron 4 of 4	1		ENSP00000461206.1
RMI2	ENST00000649869.1	n.153-58562C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs12922090; hg19: chr16-11415117;