16-11351183-G-A

Variant names:

• chr16-11351183-G-A
• rs2032933
• NM_152308.3:c.*393G>A

Variant summary

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

The NM_152308.3(RMI2):​c.*393G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 238,306 control chromosomes in the GnomAD database, including 84,247 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 0.84 (53746 hom., cov: 33)
  • Exomes 𝑓: 0.84 (30501 hom.)
• Consequence: RMI2 NM_152308.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 18 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152308.3. 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
	RMI2	NM_152308.3	MANE Select	c.*393G>A		3_prime_UTR	Exon 2 of 2	NP_689521.1
	RMI2	NR_130754.2		n.627G>A		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000312499.6	TSL:1 MANE Select	c.*393G>A		3_prime_UTR	Exon 2 of 2	ENSP00000310356.5
	RMI2	ENST00000572173.1	TSL:1	c.*393G>A		3_prime_UTR	Exon 5 of 5	ENSP00000461206.1
	RMI2	ENST00000576027.1	TSL:2	c.*530G>A		3_prime_UTR	Exon 2 of 2	ENSP00000459601.1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127703 AN: 152096 Hom.: 53696 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.865

GnomAD4 exome AF: 0.840 AC: 72323 AN: 86092 Hom.: 30501 Cov.: 0 AF XY: 0.839 AC XY: 33656 AN XY: 40112

African (AFR) AF: 0.858 AC: 3381 AN: 3940

American (AMR) AF: 0.894 AC: 2416 AN: 2702

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 4440 AN: 5204

East Asian (EAS) AF: 0.951 AC: 10870 AN: 11434

South Asian (SAS) AF: 0.887 AC: 1430 AN: 1612

European-Finnish (FIN) AF: 0.858 AC: 285 AN: 332

Middle Eastern (MID) AF: 0.911 AC: 461 AN: 506

European-Non Finnish (NFE) AF: 0.810 AC: 43172 AN: 53318

Other (OTH) AF: 0.833 AC: 5868 AN: 7044

GnomAD4 genome AF: 0.840 AC: 127811 AN: 152214 Hom.: 53746 Cov.: 33 AF XY: 0.845 AC XY: 62900 AN XY: 74396

African (AFR) AF: 0.853 AC: 35424 AN: 41544

American (AMR) AF: 0.884 AC: 13509 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4904 AN: 5186

South Asian (SAS) AF: 0.880 AC: 4246 AN: 4826

European-Finnish (FIN) AF: 0.853 AC: 9027 AN: 10580

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54909 AN: 68010

Other (OTH) AF: 0.866 AC: 1833 AN: 2116

Alfa AF: 0.824 Hom.: 75602

Bravo AF: 0.841

Asia WGS AF: 0.920 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.11
DANN	Benign	0.67
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2032933; hg19: chr16-11445040;