dbSNP rs2032933: RMI2:c.*393G>A (chr16-11351183-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

18 publications found

Variant links:

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]

RMI2 links:

LOC105371082 (HGNC:):

LOC105371082 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
RMI2	NM_152308.3 link	c.*393G>A	3_prime_UTR_variant	Exon 2 of 2	ENST00000312499.6	NP_689521.1	Q96E14-1
RMI2	NR_130754.2 link	n.627G>A	non_coding_transcript_exon_variant	Exon 2 of 2
LOC105371082	XR_933070.4 link	n.179-28639G>A	intron_variant	Intron 1 of 2
LOC105371082	XR_933073.3 link	n.810-28639G>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000312499.6 link	c.*393G>A		3_prime_UTR_variant	Exon 2 of 2	1	NM_152308.3	ENSP00000310356.5		Q96E14-1

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127703

AN:

152096

Hom.:

53696

Cov.:

show subpopulations

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.:

AF XY:

0.839

AC XY:

33656

AN XY:

40112

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

582

1164

1745

2327

2909

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

150

300

450

600

750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.840

AC:

127811

AN:

152214

Hom.:

53746

Cov.:

AF XY:

0.845

AC XY:

62900

AN XY:

74396

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1060

2120

3181

4241

5301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.11

(source)

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over