Variant rs33977706 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000572173.1(RMI2):c.-516+6520C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,236 control chromosomes in the GnomAD database, including 4,199 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 0.21 ( 4175 hom., cov: 32)

Exomes 𝑓: 0.28 ( 24 hom. )

Consequence

RMI2
ENST00000572173.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.341

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4 link	n.178+6520C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
RMI2	ENST00000572173.1 link	c.-516+6520C>A	intron_variant	1	ENSP00000461206.1	Q96E14-2
RMI2	ENST00000573910.1 link	n.160+6520C>A	intron_variant	3
RMI2	ENST00000649869.1 link	n.152+6520C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32206

AN:

151750

Hom.:

4177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0682

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.173

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.278

AC:

104

AN:

374

Hom.:

AF XY:

0.293

AC XY:

AN XY:

270

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.389

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.400

GnomAD4 genome

AF:

0.212

AC:

32185

AN:

151862

Hom.:

4175

Cov.:

AF XY:

0.211

AC XY:

15686

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.0680

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.254

Gnomad4 SAS

AF:

0.172

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.205

Hom.:

1180

Bravo

AF:

0.195

Asia WGS

AF:

0.192

AC:

664

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

5.6

DANN

Benign

0.82

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