13-91352883-C-T

Position:

• chr13-91352883-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NR_027350.1(MIR17HG):​n.3326C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,662 control chromosomes in the GnomAD database, including 18,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.47 (18387 hom., cov: 29)
• Consequence: MIR17HG NR_027350.1 non_coding_transcript_exon
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.480

Genes affected

MIR17HG (HGNC:23564): (miR-17-92a-1 cluster host gene) This gene is the host gene for the MIR17-92 cluster, a group of at least six microRNAs (miRNAs) that may be involved in cell survival, proliferation, differentiation, and angiogenesis. Amplification of this gene has been found in several lymphomas and solid tumors. Two non-protein coding transcript variants have been found for this host gene, but only the longest is a polycistronic transcript containing the MIR17-92 cluster. [provided by RefSeq, May 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 13-91352883-C-T is Benign according to our data. Variant chr13-91352883-C-T is described in ClinVar as [Benign]. Clinvar id is 3060743.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR17HG	NR_027350.1	n.3326C>T		non_coding_transcript_exon_variant	2/2
MIR17HG	NR_027349.1	n.285-1050C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000710422.1	n.407+2657C>T		intron_variant, non_coding_transcript_variant
	ENST00000710739.1	n.1036-35G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71506 AN: 151546 Hom.: 18375 Cov.: 29

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.472 AC: 71523 AN: 151662 Hom.: 18387 Cov.: 29 AF XY: 0.472 AC XY: 34937 AN XY: 74086

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.515

Alfa AF: 0.496 Hom.: 2451

Bravo AF: 0.473

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

MIR17HG-related disorder Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7336610; hg19: chr13-92005137;