chr16-11260640-T-C

Variant names:

• chr16-11260640-T-C
• rs243325
• ENST00000572173.1:c.-516+10862T>C

Variant summary

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

The ENST00000572173.1(RMI2):​c.-516+10862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,032 control chromosomes in the GnomAD database, including 11,999 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 0.38 (11999 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 21 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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+10862T>C		intron	N/A	ENSP00000461206.1
	RMI2	ENST00000573910.1	TSL:3	n.160+10862T>C		intron	N/A
	RMI2	ENST00000649869.1		n.152+10862T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57997 AN: 151914 Hom.: 11969 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.382 AC: 58082 AN: 152032 Hom.: 11999 Cov.: 32 AF XY: 0.391 AC XY: 29080 AN XY: 74318

African (AFR) AF: 0.410 AC: 16983 AN: 41446

American (AMR) AF: 0.498 AC: 7617 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3750 AN: 5154

South Asian (SAS) AF: 0.591 AC: 2847 AN: 4814

European-Finnish (FIN) AF: 0.331 AC: 3495 AN: 10568

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21097 AN: 67992

Other (OTH) AF: 0.361 AC: 760 AN: 2106

Alfa AF: 0.358 Hom.: 20941

Bravo AF: 0.400

Asia WGS AF: 0.617 AC: 2144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		-0.072
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: rs243325; hg19: chr16-11354497;