rs33989964

Variant names:

• chr16-11256954-CTG-C
• rs33989964
• ENST00000572173.1:c.-516+7177_-516+7178delTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000572173.1(RMI2):​c.-516+7177_-516+7178delTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,108 control chromosomes in the GnomAD database, including 4,427 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4427 hom., cov: 26)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572173.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000572173.1	TSL:1	c.-516+7177_-516+7178delTG		intron	N/A	ENSP00000461206.1
	RMI2	ENST00000573910.1	TSL:3	n.160+7177_160+7178delTG		intron	N/A
	RMI2	ENST00000649869.1		n.152+7177_152+7178delTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35100 AN: 151990 Hom.: 4423 Cov.: 26

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.231 AC: 35127 AN: 152108 Hom.: 4427 Cov.: 26 AF XY: 0.231 AC XY: 17142 AN XY: 74342

African (AFR) AF: 0.151 AC: 6259 AN: 41506

American (AMR) AF: 0.173 AC: 2649 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3470

East Asian (EAS) AF: 0.139 AC: 721 AN: 5180

South Asian (SAS) AF: 0.333 AC: 1604 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2969 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18970 AN: 67954

Other (OTH) AF: 0.236 AC: 499 AN: 2114

Alfa AF: 0.267 Hom.: 672

Bravo AF: 0.220

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.1
Mutation Taster		=88/12	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs33989964; hg19: chr16-11350811;