rs2858059

Variant names:

• chrX-45747784-G-A
• rs2858059
• NR_170290.1:n.22352C>T

Variant summary

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

The NR_170290.1(MIR222HG):​n.22352C>T 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 0.374 in 110,513 control chromosomes in the GnomAD database, including 8,840 homozygotes. There are 11,928 hemizygotes in GnomAD. 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 0.37 (8840 hom., 11928 hem., cov: 22)
• Consequence: MIR222HG NR_170290.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR222HG	NR_170290.1	n.22352C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR222HG	ENST00000602461.1	n.490-1684C>T		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.373 AC: 41256 AN: 110459 Hom.: 8833 Cov.: 22 AF XY: 0.363 AC XY: 11879 AN XY: 32711

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.0408

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.374 AC: 41316 AN: 110513 Hom.: 8840 Cov.: 22 AF XY: 0.364 AC XY: 11928 AN XY: 32775

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.369

Alfa AF: 0.248 Hom.: 2806

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.074

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858059; hg19: chrX-45607190;