rs1019553

Variant names:

• chr16-11302493-C-A
• rs1019553
• ENST00000572173.1:c.-437+7199C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-11302493-C-A
• chr16-11302493-C-T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-437+7199C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 152,192 control chromosomes in the GnomAD database, including 813 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 0.097 (813 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 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.-437+7199C>A		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.161-13959C>A		intron	N/A
	RMI2	ENST00000649869.1		n.152+52715C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14790 AN: 152074 Hom.: 806 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0973 AC: 14812 AN: 152192 Hom.: 813 Cov.: 32 AF XY: 0.0994 AC XY: 7398 AN XY: 74396

African (AFR) AF: 0.0871 AC: 3618 AN: 41526

American (AMR) AF: 0.0689 AC: 1052 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3470

East Asian (EAS) AF: 0.0898 AC: 466 AN: 5188

South Asian (SAS) AF: 0.180 AC: 868 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1256 AN: 10588

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0967 AC: 6574 AN: 68014

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.0971 Hom.: 1053

Bravo AF: 0.0923

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1019553;

hg19: chr16-11396350;