rs9673543

Variant names:

• chr16-11291099-A-G
• rs9673543
• ENST00000572173.1:c.-515-4117A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-11291099-A-G
• chr16-11291099-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000572173.1(RMI2):​c.-515-4117A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,980 control chromosomes in the GnomAD database, including 7,041 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 0.27 (7041 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339

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]

ENSG00000287429 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+41321A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-4117A>G		intron_variant	Intron 1 of 4	1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.161-25353A>G		intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1	n.152+41321A>G		intron_variant	Intron 1 of 2
ENSG00000287429	ENST00000653530.1	n.189+342A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41609 AN: 151860 Hom.: 7020 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.274 AC: 41669 AN: 151980 Hom.: 7041 Cov.: 31 AF XY: 0.287 AC XY: 21354 AN XY: 74304

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.263

Alfa AF: 0.239 Hom.: 705

Bravo AF: 0.292

Asia WGS AF: 0.554 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9673543; hg19: chr16-11384956;