chr20-62564810-G-T

Variant names:

• chr20-62564810-G-T
• rs45547937
• ENST00000624914.4:n.794-179G>T

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 0 publications found

Genes affected

MIR1-1HG (HGNC:16159): (MIR1-1 host gene) Predicted to be involved in miRNA-mediated post-transcriptional gene silencing. Predicted to be part of RISC complex. [provided by Alliance of Genome Resources, Jun 2026]

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]

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = 0.000136, AC = 0 — absent/extremely rare (O3 moderate [+2])

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	Intron 2 of 3	Prot:
	MIR133A2 NR_029676.1		n.-102G>T	upstream_gene	N/A	Prot:

MIR1-1HG NR_171007.1

HGVSc / HGVSpn.788-179G>T

Exon rankIntron 2 of 3

intron

Prot:

MIR133A2 NR_029676.1

HGVSc / HGVSpn.-102G>T

Exon rankN/A

upstream_gene

Prot:

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	MIR1-1HG ENST00000624914.4	TSL:1	n.794-179G>T	intron	Intron 2 of 3	Prot:
	MIR1-1HG ENST00000370523.4	TSL:5	n.244-5634G>T	intron	Intron 2 of 2	Prot:
	MIR1-1HG ENST00000686477.2		n.793-5634G>T	intron	Intron 2 of 2	Prot:

MIR1-1HG ENST00000624914.4

TSL:1

HGVSc / HGVSpn.794-179G>T

Exon rankIntron 2 of 3

intron

Prot:

MIR1-1HG ENST00000370523.4

TSL:5

HGVSc / HGVSpn.244-5634G>T

Exon rankIntron 2 of 2

intron

Prot:

MIR1-1HG ENST00000686477.2

HGVSc / HGVSpn.793-5634G>T

Exon rankIntron 2 of 2

intron

Prot:

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 pred.	Score	Prediction
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.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs45547937;

hg19: chr20-61162017;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar