dbSNP rs7191700: RMI2:c.-328+9C>T (chr16-11312946-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000572173.1(RMI2):c.-328+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,228 control chromosomes in the GnomAD database, including 5,912 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 0.27 ( 5908 hom., cov: 32)

Exomes 𝑓: 0.28 ( 4 hom. )

Consequence

RMI2
ENST00000572173.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4 link	n.178+63168C>T		intron_variant	Intron 1 of 2
LOC105371082	XR_933073.3 link	n.65+9C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
RMI2	ENST00000572173.1 link	c.-328+9C>T	intron_variant	Intron 3 of 4	1	ENSP00000461206.1	Q96E14-2
RMI2	ENST00000572992.1 link	n.38+9C>T	intron_variant	Intron 1 of 1	2
RMI2	ENST00000573910.1 link	n.161-3506C>T	intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1 link	n.152+63168C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40411

AN:

152056

Hom.:

5904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.0494

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.270

GnomAD4 exome

AF:

0.278

AC:

AN:

Hom.:

Cov.:

AF XY:

0.237

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.266

AC:

40431

AN:

152174

Hom.:

5908

Cov.:

AF XY:

0.259

AC XY:

19290

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.181

Gnomad4 AMR

AF:

0.214

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.0495

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.327

Hom.:

17522

Bravo

AF:

0.258

Asia WGS

AF:

0.137

AC:

480

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

4.0

DANN

Benign

0.85

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over