rs529866

Positions:

• chr16-11279463-C-T

Variant summary

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

The XR_933070.4(LOC105371082):​n.178+29685C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,078 control chromosomes in the GnomAD database, including 2,538 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 0.18 (2538 hom., cov: 31)
• Consequence: LOC105371082 XR_933070.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+29685C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-15753C>T		intron_variant		1		ENSP00000461206
RMI2	ENST00000573910.1	n.160+29685C>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+29685C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27302 AN: 151960 Hom.: 2528 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.180 AC: 27339 AN: 152078 Hom.: 2538 Cov.: 31 AF XY: 0.174 AC XY: 12938 AN XY: 74356

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.149

Alfa AF: 0.184 Hom.: 460

Bravo AF: 0.180

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs529866; hg19: chr16-11373320;