rs12927773

chr16-11310106-G-T

Variant summary

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

The ENST00000572173.1(RMI2):c.-436-2723G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,236 control chromosomes in the GnomAD database, including 1,530 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 0.14 (1530 hom., cov: 33)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371082	XR_933070.4	n.178+60328G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMI2	ENST00000572173.1	c.-436-2723G>T		intron_variant		1
RMI2	ENST00000573910.1	n.161-6346G>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+60328G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21254 AN: 152118 Hom.: 1529 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.140 AC: 21266 AN: 152236 Hom.: 1530 Cov.: 33 AF XY: 0.136 AC XY: 10083 AN XY: 74412

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.117

Alfa AF: 0.154 Hom.: 959

Bravo AF: 0.138

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.2
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12927773; hg19: chr16-11403963;