rs1019553

chr16-11302493-C-Achr16-11302493-C-T

Variant summary

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

The ENST00000572173.1(RMI2):c.-437+7199C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 152,192 control chromosomes in the GnomAD database, including 813 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 0.097 (813 hom., cov: 32)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371082	XR_933070.4	n.178+52715C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMI2	ENST00000572173.1	c.-437+7199C>A		intron_variant		1
RMI2	ENST00000573910.1	n.161-13959C>A		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+52715C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0973 AC: 14790 AN: 152074 Hom.: 806 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0973 AC: 14812 AN: 152192 Hom.: 813 Cov.: 32 AF XY: 0.0994 AC XY: 7398 AN XY: 74396

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0898

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0967

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0966 Hom.: 788

Bravo AF: 0.0923

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1019553; hg19: chr16-11396350;