rs2032933

chr16-11351183-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMI2	NM_152308.3	c.*393G>A		3_prime_UTR_variant	2/2	ENST00000312499.6
LOC105371082	XR_933070.4	n.179-28639G>A		intron_variant, non_coding_transcript_variant
RMI2	NR_130754.2	n.627G>A		non_coding_transcript_exon_variant	2/2
LOC105371082	XR_933073.3	n.810-28639G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMI2	ENST00000312499.6	c.*393G>A		3_prime_UTR_variant	2/2	1	NM_152308.3	P1

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

Gnomad4 AFR exome AF: 0.858

Gnomad4 AMR exome AF: 0.894

Gnomad4 ASJ exome AF: 0.853

Gnomad4 EAS exome AF: 0.951

Gnomad4 SAS exome AF: 0.887

Gnomad4 FIN exome AF: 0.858

Gnomad4 NFE exome AF: 0.810

Gnomad4 OTH exome AF: 0.833

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

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.866

Alfa AF: 0.821 Hom.: 50644

Bravo AF: 0.841

Asia WGS AF: 0.920 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.11
Dann	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032933; hg19: chr16-11445040;