ENST00000582141.6:n.3584C>A

Variant names:

• chr13-91353141-C-A
• rs1875410050
• ENST00000582141.6:n.3584C>A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP6

The ENST00000582141.6(MIR17HG):​n.3584C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.00041 (0 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: MIR17HG ENST00000582141.6 non_coding_transcript_exon
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.654

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]

ENSG00000292285 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 13-91353141-C-A is Benign according to our data. Variant chr13-91353141-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3032970.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR17HG	NR_027350.2	n.3717C>A		non_coding_transcript_exon_variant	Exon 2 of 2
MIR17HG	NR_197388.1	n.3332C>A		non_coding_transcript_exon_variant	Exon 3 of 3
MIR17HG	NR_027349.2	n.418-792C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR17HG	ENST00000582141.6	n.3584C>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
MIR17HG	ENST00000400282.7	n.285-792C>A		intron_variant	Intron 3 of 3	1
MIR17HG	ENST00000710419.1	n.771C>A		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 53 AN: 130888 Hom.: 0 Cov.: 29 FAILED QC

Gnomad AFR AF: 0.000366

Gnomad AMI AF: 0.00120

Gnomad AMR AF: 0.000474

Gnomad ASJ AF: 0.000310

Gnomad EAS AF: 0.00143

Gnomad SAS AF: 0.00130

Gnomad FIN AF: 0.000613

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000274

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000412 AC: 54 AN: 130924 Hom.: 0 Cov.: 29 AF XY: 0.000478 AC XY: 30 AN XY: 62778

Gnomad4 AFR AF: 0.000366

Gnomad4 AMR AF: 0.000552

Gnomad4 ASJ AF: 0.000310

Gnomad4 EAS AF: 0.00143

Gnomad4 SAS AF: 0.00130

Gnomad4 FIN AF: 0.000613

Gnomad4 NFE AF: 0.000274

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

MIR17HG-related disorder Benign:1

Aug 30, 2023

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely 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	-0.86
CADD	Benign	0.63
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1875410050; hg19: chr13-92005395;