ENST00000572173.1:c.-515-9298T>C

Variant names:

• chr16-11285918-T-C
• rs1794019
• ENST00000572173.1:c.-515-9298T>C

Variant summary

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

The ENST00000572173.1(RMI2):​c.-515-9298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,274 control chromosomes in the GnomAD database, including 1,565 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 0.13 (1565 hom., cov: 33)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+36140T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-9298T>C		intron_variant	Intron 1 of 4	1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.161-30534T>C		intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1	n.152+36140T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19454 AN: 152156 Hom.: 1563 Cov.: 33

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.128 AC: 19458 AN: 152274 Hom.: 1565 Cov.: 33 AF XY: 0.124 AC XY: 9217 AN XY: 74460

African (AFR) AF: 0.0344 AC: 1428 AN: 41566

American (AMR) AF: 0.102 AC: 1555 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.0466 AC: 242 AN: 5190

South Asian (SAS) AF: 0.125 AC: 602 AN: 4826

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13102 AN: 68014

Other (OTH) AF: 0.114 AC: 240 AN: 2110

Alfa AF: 0.157 Hom.: 258

Bravo AF: 0.122

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-0.078
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: rs1794019; hg19: chr16-11379775;