chrX-45746704-C-G

Variant names:

• chrX-45746704-C-G
• rs2858061
• ENST00000688264.3:n.900G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_170290.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR222HG	NR_170290.1		n.23432G>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR222HG	ENST00000688264.3		n.900G>C		non_coding_transcript_exon	Exon 4 of 4
	MIR222HG	ENST00000602461.1	TSL:5	n.490-604G>C		intron	N/A
	MIR222HG	ENST00000715684.1		n.445-968G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 29732 AN: 109147 Hom.: 4113 Cov.: 20

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

African (AFR) AF: 0.432 AC: 12882 AN: 29797

American (AMR) AF: 0.403 AC: 4121 AN: 10232

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 366 AN: 2612

East Asian (EAS) AF: 0.794 AC: 2704 AN: 3407

South Asian (SAS) AF: 0.434 AC: 1068 AN: 2459

European-Finnish (FIN) AF: 0.153 AC: 890 AN: 5800

Middle Eastern (MID) AF: 0.204 AC: 42 AN: 206

European-Non Finnish (NFE) AF: 0.137 AC: 7197 AN: 52500

Other (OTH) AF: 0.302 AC: 453 AN: 1502

Alfa AF: 0.0859 Hom.: 436

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2858061; hg19: chrX-45606132;