ENST00000572173.1:c.-515-5554T>C

Variant names:

• chr16-11289662-T-C
• rs4451969
• ENST00000572173.1:c.-515-5554T>C

Variant summary

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

The ENST00000572173.1(RMI2):​c.-515-5554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,814 control chromosomes in the GnomAD database, including 25,492 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 0.56 (25492 hom., cov: 30)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 13 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 = 0.663 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMI2	ENST00000572173.1	TSL:1	c.-515-5554T>C		intron	N/A	ENSP00000461206.1
	RMI2	ENST00000573910.1	TSL:3	n.161-26790T>C		intron	N/A
	RMI2	ENST00000649869.1		n.152+39884T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85744 AN: 151696 Hom.: 25495 Cov.: 30

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.565 AC: 85761 AN: 151814 Hom.: 25492 Cov.: 30 AF XY: 0.558 AC XY: 41395 AN XY: 74152

African (AFR) AF: 0.439 AC: 18188 AN: 41384

American (AMR) AF: 0.485 AC: 7385 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5166

South Asian (SAS) AF: 0.426 AC: 2048 AN: 4802

European-Finnish (FIN) AF: 0.657 AC: 6934 AN: 10546

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.668 AC: 45384 AN: 67910

Other (OTH) AF: 0.613 AC: 1289 AN: 2102

Alfa AF: 0.618 Hom.: 20561

Bravo AF: 0.543

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		0.19
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: rs4451969; hg19: chr16-11383519;