chr16-11257134-C-T

Variant names:

• chr16-11257134-C-T
• rs243330
• ENST00000572173.1:c.-516+7356C>T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-516+7356C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,794 control chromosomes in the GnomAD database, including 19,363 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 0.50 (19363 hom., cov: 30)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 20 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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.-516+7356C>T		intron	N/A	ENSP00000461206.1	Q96E14-2
	RMI2	ENST00000573910.1	TSL:3	n.160+7356C>T		intron	N/A
	RMI2	ENST00000649869.1		n.152+7356C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75408 AN: 151676 Hom.: 19316 Cov.: 30

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.497 AC: 75511 AN: 151794 Hom.: 19363 Cov.: 30 AF XY: 0.504 AC XY: 37357 AN XY: 74168

African (AFR) AF: 0.481 AC: 19912 AN: 41368

American (AMR) AF: 0.608 AC: 9276 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2039 AN: 3464

East Asian (EAS) AF: 0.736 AC: 3790 AN: 5152

South Asian (SAS) AF: 0.680 AC: 3268 AN: 4804

European-Finnish (FIN) AF: 0.435 AC: 4584 AN: 10542

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31086 AN: 67904

Other (OTH) AF: 0.503 AC: 1057 AN: 2100

Alfa AF: 0.483 Hom.: 2833

Bravo AF: 0.513

Asia WGS AF: 0.676 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.18
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: rs243330;

hg19: chr16-11350991;