rs9860655

Positions:

• chr3-195699434-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

Genes affected

MIR570 (HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR570	NR_030296.1	n.34T>C		non_coding_transcript_exon_variant	1/1
MIR570	unassigned_transcript_716	n.10T>C		non_coding_transcript_exon_variant	1/1
MIR570HG	NR_122105.1	n.401-8700T>C		intron_variant
MIR570	unassigned_transcript_717	n.-26T>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR570	ENST00000384917.1	n.34T>C		non_coding_transcript_exon_variant	1/1	6
MUC20-OT1	ENST00000420851.6	n.515-8700T>C		intron_variant		5
MUC20-OT1	ENST00000431767.5	n.152-8700T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0781 AC: 11456 AN: 146672 Hom.: 0 Cov.: 44

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.: 1 AF XY: 0.107 AC XY: 12498 AN XY: 116912

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.: 2 Cov.: 0 AF XY: 0.121 AC XY: 24167 AN XY: 200056

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.: 0 Cov.: 44 AF XY: 0.0768 AC XY: 5502 AN XY: 71678

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.: 0

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

Other links and lift over

dbSNP: rs9860655; hg19: chr3-195426305;