rs12922090

Positions:

• chr16-11321260-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105371082	XR_933070.4	n.179-58562C>T		intron_variant, non_coding_transcript_variant
LOC105371082	XR_933073.3	n.809+4376C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMI2	ENST00000572173.1	c.106+4376C>T		intron_variant		1
RMI2	ENST00000649869.1	n.153-58562C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0299

Gnomad4 AMR AF: 0.0936

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.101

Alfa AF: 0.136 Hom.: 262

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12922090; hg19: chr16-11415117;