chrX-45747602-G-C

Variant names:

• chrX-45747602-G-C
• rs2858060
• ENST00000780196.1:n.813C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000780196.1(MIR222HG):​n.813C>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 ENST00000780196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 8 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 (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 rank	MANE	Protein	UniProt
MIR222HG	NR_170290.1	n.22534C>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR222HG	ENST00000780196.1	n.813C>G		non_coding_transcript_exon_variant	Exon 4 of 4
MIR222HG	ENST00000602461.1	n.490-1502C>G		intron_variant	Intron 1 of 1	5
MIR222HG	ENST00000688264.3	n.449-447C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 42557 AN: 111025 Hom.: 6232 Cov.: 23

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

African (AFR) AF: 0.458 AC: 13966 AN: 30521

American (AMR) AF: 0.477 AC: 4995 AN: 10479

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 678 AN: 2640

East Asian (EAS) AF: 0.802 AC: 2805 AN: 3498

South Asian (SAS) AF: 0.574 AC: 1538 AN: 2681

European-Finnish (FIN) AF: 0.280 AC: 1656 AN: 5908

Middle Eastern (MID) AF: 0.375 AC: 81 AN: 216

European-Non Finnish (NFE) AF: 0.305 AC: 16156 AN: 52935

Other (OTH) AF: 0.396 AC: 603 AN: 1522

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2858060; hg19: -;