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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+7177_178+7178delTG		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-516+7177_-516+7178delTG		intron_variant	Intron 1 of 4	1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.160+7177_160+7178delTG		intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1	n.152+7177_152+7178delTG		intron_variant	Intron 1 of 2

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 v4.3

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;