rs181694

chr16-11290972-C-T

Variant summary

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

The ENST00000572173.1(RMI2):c.-515-4244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,046 control chromosomes in the GnomAD database, including 1,986 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 0.16 (1986 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371082	XR_933070.4	n.178+41194C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-4244C>T		intron_variant		1
	ENST00000653530.1	n.189+215C>T		intron_variant, non_coding_transcript_variant
RMI2	ENST00000573910.1	n.161-25480C>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+41194C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24446 AN: 151928 Hom.: 1983 Cov.: 31

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.161 AC: 24461 AN: 152046 Hom.: 1986 Cov.: 31 AF XY: 0.156 AC XY: 11605 AN XY: 74320

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0475

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.132

Alfa AF: 0.179 Hom.: 1453

Bravo AF: 0.159

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	10
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181694; hg19: chr16-11384829;