rs2858061

Positions:

• chrX-45746704-C-G
• chrX-45746704-C-T

Variant summary

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

The NR_170290.1(MIR222HG):​n.23432G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.27 (4117 hom., 8417 hem., cov: 20)
• Consequence: MIR222HG NR_170290.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

MIR222HG (HGNC:49555): (miR222/221 cluster host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR222HG	NR_170290.1	n.23432G>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR222HG	ENST00000602461.1	n.490-604G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 29732 AN: 109147 Hom.: 4113 Cov.: 20 AF XY: 0.267 AC XY: 8402 AN XY: 31511

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.0427

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.272 AC: 29752 AN: 109194 Hom.: 4117 Cov.: 20 AF XY: 0.267 AC XY: 8417 AN XY: 31568

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.302

Alfa AF: 0.0859 Hom.: 436

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858061; hg19: chrX-45606132;