ENST00000581816.1:n.1454_1458delCTTGT
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2
The ENST00000581816.1(MIR17HG):n.1454_1458delCTTGT 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 0.0000215 in 232,652 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000581816.1 non_coding_transcript_exon
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MIR17HG | NR_027350.2 | n.2094_2098delCTTGT | non_coding_transcript_exon_variant | Exon 2 of 2 | ||||
MIR17HG | NR_197388.1 | n.1709_1713delCTTGT | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
MIR17HG | NR_027349.2 | n.417+1292_417+1296delCTTGT | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIR17HG | ENST00000581816.1 | n.1454_1458delCTTGT | non_coding_transcript_exon_variant | Exon 3 of 3 | 1 | |||||
MIR17HG | ENST00000582141.6 | n.1961_1965delCTTGT | non_coding_transcript_exon_variant | Exon 2 of 2 | 1 | |||||
MIR17HG | ENST00000400282.7 | n.284+1292_284+1296delCTTGT | intron_variant | Intron 3 of 3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152230Hom.: 0 Cov.: 33 FAILED QC
GnomAD4 exome AF: 0.0000215 AC: 5AN: 232652Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126774
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
MIR17HG-related disorder Uncertain:1
The MIR17HG n.1961_1965del5 variant is predicted to result in an in-frame deletion (Non-Coding). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at