16-11258456-A-T

Variant names:

• chr16-11258456-A-T
• rs243329
• ENST00000572173.1:c.-516+8678A>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-516+8678A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,774 control chromosomes in the GnomAD database, including 20,798 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 0.52 (20798 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.712 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+8678A>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.160+8678A>T		intron	N/A
	RMI2	ENST00000649869.1		n.152+8678A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78366 AN: 151656 Hom.: 20748 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.517 AC: 78472 AN: 151774 Hom.: 20798 Cov.: 31 AF XY: 0.523 AC XY: 38796 AN XY: 74168

African (AFR) AF: 0.523 AC: 21602 AN: 41300

American (AMR) AF: 0.618 AC: 9433 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2042 AN: 3464

East Asian (EAS) AF: 0.731 AC: 3786 AN: 5176

South Asian (SAS) AF: 0.683 AC: 3287 AN: 4810

European-Finnish (FIN) AF: 0.450 AC: 4747 AN: 10538

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 31996 AN: 67912

Other (OTH) AF: 0.511 AC: 1077 AN: 2108

Alfa AF: 0.493 Hom.: 2227

Bravo AF: 0.533

Asia WGS AF: 0.680 AC: 2365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.42
PhyloP100		-1.3
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: rs243329; hg19: chr16-11352313;