ENST00000572173.1:c.-436-2723G>T

Variant names:

• chr16-11310106-G-T
• rs12927773
• ENST00000572173.1:c.-436-2723G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 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=-0.94).
• 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 rank	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+60328G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-436-2723G>T		intron_variant	Intron 2 of 4	1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.161-6346G>T		intron_variant	Intron 1 of 1	3
RMI2	ENST00000649869.1	n.152+60328G>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.129 AC: 5365 AN: 41560

American (AMR) AF: 0.0949 AC: 1451 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 432 AN: 3470

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5184

South Asian (SAS) AF: 0.102 AC: 493 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10586

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11358 AN: 68008

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.155 Hom.: 1309

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
PhyloP100		-0.69
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: rs12927773; hg19: chr16-11403963;