rs33989964

Positions:

• chr16-11256954-CTG-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+7177_178+7178delTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-516+7177_-516+7178delTG		intron_variant		1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.160+7177_160+7178delTG		intron_variant		3
RMI2	ENST00000649869.1	n.152+7177_152+7178delTG		intron_variant

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.236

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33989964; hg19: chr16-11350811;