chr16-11277902-C-T

Position:

• chr16-11277902-C-T

Variant summary

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

The ENST00000572173.1(RMI2):​c.-515-17314C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,192 control chromosomes in the GnomAD database, including 1,535 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 0.13 (1535 hom., cov: 31)
• Consequence: RMI2 ENST00000572173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+28124C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-17314C>T		intron_variant		1		ENSP00000461206
RMI2	ENST00000573910.1	n.160+28124C>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+28124C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19318 AN: 152074 Hom.: 1533 Cov.: 31

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.127 AC: 19322 AN: 152192 Hom.: 1535 Cov.: 31 AF XY: 0.123 AC XY: 9160 AN XY: 74398

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0478

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.114

Alfa AF: 0.160 Hom.: 255

Bravo AF: 0.121

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.71
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs441349; hg19: chr16-11371759;