20-62564810-G-T

Variant names:

Variant summary

Our verdict is The variant received -3 classification points (ACMG Germline Pathogenicity v2019). PM2_SupportingBP4_Strong

The NR_171007.1(MIR1-1HG):n.788-179G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: NR_171007.1 is not a MANE Select or MANE Plus Clinical transcript for MIR1-1HG; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant has a gnomAD grpmax filtering allele frequency (95% CI) of 0.000136, indicating it is observed in the general population. Note: a gnomAD entry for this variant shows a statistical allele-bias signature, consistent with mosaic/somatic contamination (e.g. age-related clonal hematopoiesis) rather than true inherited population frequency — this frequency should not be read as evidence of a common, benign germline variant. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 35)

Exomes 𝑓: 0.0000047 ( 0 hom. )

Consequence

MIR1-1HG
NR_171007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809

Publications

0 publications found

Variant links:

Genes affected

MIR1-1HG (HGNC:16159): (MIR1-1 host gene)

MIR1-1HG links:

MIR133A2 (HGNC:31518): (microRNA 133a-2) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR133A2 links:

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new If you want to explore the variant's impact on the transcript NR_171007.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -3 points.

Show applied only (2)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Rare in gnomAD for AR/unknown gene (popmax AF below threshold) — PM2 Supporting; GnomAD popmax AF = 0.000136 — borderline rare for unknown gene (threshold 0.001) — PM2 supporting.
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NR_171007.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR1-1HG	NR_171007.1		n.788-179G>T		intron	N/A
	MIR133A2	NR_029676.1		n.-102G>T		upstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIR1-1HG	ENST00000624914.4	TSL:1	n.794-179G>T	intron	N/A
MIR1-1HG	ENST00000370523.4	TSL:5	n.244-5634G>T	intron	N/A
MIR1-1HG	ENST00000686477.2		n.793-5634G>T	intron	N/A

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:35
GnomAD4 exome Warning	AF: 0.00000472	AC:1	Hom:0	AN:211644	Cov:
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:35

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated prediction	Prediction	Score
AlphaGenome AVI	Benign	-	4.4
BayesDel_noAF	Benign	-	-0.94
CADD	Benign	-	1.3
DANN	Benign	-	0.64
GPN-Star LLR	N/A	-	-0.41
GPN-Star score	N/A	-	0.41
PhyloP100	Benign	-	-0.81

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

Publications

Other links and lift over