X-45747602-G-C

Position:

• chrX-45747602-G-C

Variant summary

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

The NR_170290.1(MIR222HG):​n.22534C>G 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 0.383 in 111,076 control chromosomes in the GnomAD database, including 6,234 homozygotes. There are 12,712 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 0.38 (6234 hom., 12712 hem., cov: 23)
• Consequence: MIR222HG NR_170290.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532

Genes affected

MIR222HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=5.014).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR222HG	NR_170290.1	n.22534C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR222HG	ENST00000602461.1	n.490-1502C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42557 AN: 111025 Hom.: 6232 Cov.: 23 AF XY: 0.381 AC XY: 12690 AN XY: 33295

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.383 AC: 42577 AN: 111076 Hom.: 6234 Cov.: 23 AF XY: 0.381 AC XY: 12712 AN XY: 33356

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.396

Alfa AF: 0.150 Hom.: 651

Bravo AF: 0.409

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	5.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2858060; hg19: -;