16-11257134-C-T

Position:

• chr16-11257134-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+7356C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-516+7356C>T		intron_variant		1		ENSP00000461206.1
RMI2	ENST00000573910.1	n.160+7356C>T		intron_variant		3
RMI2	ENST00000649869.1	n.152+7356C>T		intron_variant

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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.503

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243330; hg19: chr16-11350991;