Genetic Variant RMI2:c.-516+11335A>G (chr16-11261113-A-G) – 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.-516+11335A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,934 control chromosomes in the GnomAD database, including 20,864 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 0.52 ( 20864 hom., cov: 32)

Consequence

RMI2
ENST00000572173.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.671

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=-1.07).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4 link	n.178+11335A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
RMI2	ENST00000572173.1 link	c.-516+11335A>G	intron_variant	Intron 1 of 4	1	ENSP00000461206.1	Q96E14-2
RMI2	ENST00000573910.1 link	n.160+11335A>G	intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1 link	n.152+11335A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

78535

AN:

151816

Hom.:

20815

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.590

Gnomad EAS

AF:

0.732

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.451

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.506

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.518

AC:

78639

AN:

151934

Hom.:

20864

Cov.:

AF XY:

0.524

AC XY:

38893

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.524

Gnomad4 AMR

AF:

0.619

Gnomad4 ASJ

AF:

0.590

Gnomad4 EAS

AF:

0.732

Gnomad4 SAS

AF:

0.684

Gnomad4 FIN

AF:

0.451

Gnomad4 NFE

AF:

0.471

Gnomad4 OTH

AF:

0.510

Alfa

AF:

0.497

Hom.:

39011

Bravo

AF:

0.534

Asia WGS

AF:

0.680

AC:

2363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

2.5

DANN

Benign

0.30

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