chr16-11257108-G-A

Variant names:

• chr16-11257108-G-A
• rs193779
• ENST00000572173.1:c.-516+7330G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000572173.1(RMI2):​c.-516+7330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,000 control chromosomes in the GnomAD database, including 3,623 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 (3623 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 19 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000572173.1	TSL:1	c.-516+7330G>A		intron	N/A	ENSP00000461206.1
	RMI2	ENST00000573910.1	TSL:3	n.160+7330G>A		intron	N/A
	RMI2	ENST00000649869.1		n.152+7330G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32476 AN: 151882 Hom.: 3622 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00848

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.214 AC: 32471 AN: 152000 Hom.: 3623 Cov.: 31 AF XY: 0.210 AC XY: 15611 AN XY: 74296

African (AFR) AF: 0.213 AC: 8814 AN: 41430

American (AMR) AF: 0.176 AC: 2692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5176

South Asian (SAS) AF: 0.143 AC: 688 AN: 4814

European-Finnish (FIN) AF: 0.228 AC: 2409 AN: 10568

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16485 AN: 67946

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.228 Hom.: 13337

Bravo AF: 0.208

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.70
PhyloP100		0.066
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs193779; hg19: chr16-11350965;