dbSNP rs9860655: MIR570:n.34T>C (chr3-195699434-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_030296.1(MIR570):n.34T>C 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 0.102 in 500,042 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.078 ( 0 hom., cov: 44)

Exomes 𝑓: 0.11 ( 2 hom. )

Consequence

MIR570
NR_030296.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99

Variant links:

Genes affected

MIR570 (HGNC:32826): (microRNA 570) 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]

MIR570 links:

MUC20-OT1 (HGNC:53807): (MUC20 overlapping transcript)

MUC20-OT1 links:

MIR570HG (HGNC:53743): (MIR570 host gene)

MIR570HG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR570	NR_030296.1 link	n.34T>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR570	unassigned_transcript_716	n.10T>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR570HG	NR_122105.1 link	n.401-8700T>C	intron_variant	Intron 2 of 4
MIR570	unassigned_transcript_717	n.-26T>C	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR570	ENST00000384917.1 link	n.34T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
MUC20-OT1	ENST00000420851.6 link	n.515-8700T>C	intron_variant	Intron 2 of 4	5
MUC20-OT1	ENST00000431767.5 link	n.152-8700T>C	intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0781

AC:

11456

AN:

146672

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0180

Gnomad AMI

AF:

0.0695

Gnomad AMR

AF:

0.0674

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0119

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.0820

Gnomad MID

AF:

0.147

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.0977

AC:

21204

AN:

217076

Hom.:

AF XY:

0.107

AC XY:

12498

AN XY:

116912

show subpopulations

Gnomad AFR exome

AF:

0.0164

Gnomad AMR exome

AF:

0.0495

Gnomad ASJ exome

AF:

0.122

Gnomad EAS exome

AF:

0.0136

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.0824

Gnomad NFE exome

AF:

0.115

Gnomad OTH exome

AF:

0.103

GnomAD4 exome

AF:

0.112

AC:

39498

AN:

353256

Hom.:

Cov.:

AF XY:

0.121

AC XY:

24167

AN XY:

200056

show subpopulations

Gnomad4 AFR exome

AF:

0.0180

Gnomad4 AMR exome

AF:

0.0454

Gnomad4 ASJ exome

AF:

0.104

Gnomad4 EAS exome

AF:

0.0136

Gnomad4 SAS exome

AF:

0.193

Gnomad4 FIN exome

AF:

0.0849

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.104

GnomAD4 genome

AF:

0.0781

AC:

11461

AN:

146786

Hom.:

Cov.:

AF XY:

0.0768

AC XY:

5502

AN XY:

71678

show subpopulations

Gnomad4 AFR

AF:

0.0180

Gnomad4 AMR

AF:

0.0673

Gnomad4 ASJ

AF:

0.121

Gnomad4 EAS

AF:

0.0123

Gnomad4 SAS

AF:

0.180

Gnomad4 FIN

AF:

0.0820

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.0979

Alfa

AF:

0.117

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.37

DANN

Benign

0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over