ENST00000688264.3:n.282-3461C>T

Variant names:

• chrX-45773413-G-A
• rs6521038
• ENST00000688264.3:n.282-3461C>T

Variant summary

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

The ENST00000688264.3(MIR222HG):​n.282-3461C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 110,545 control chromosomes in the GnomAD database, including 5,617 homozygotes. There are 10,144 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 0.32 (5617 hom., 10144 hem., cov: 22)
• Consequence: MIR222HG ENST00000688264.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 1 publications found

Genes affected

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

ENSG00000301662 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688264.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR222HG	ENST00000688264.3		n.282-3461C>T		intron	N/A
	MIR222HG	ENST00000715684.1		n.278-3461C>T		intron	N/A
	MIR222HG	ENST00000780192.1		n.297-3461C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 35312 AN: 110492 Hom.: 5609 Cov.: 22

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.0365

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.320 AC: 35363 AN: 110545 Hom.: 5617 Cov.: 22 AF XY: 0.309 AC XY: 10144 AN XY: 32861

African (AFR) AF: 0.573 AC: 17283 AN: 30138

American (AMR) AF: 0.430 AC: 4501 AN: 10479

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 450 AN: 2637

East Asian (EAS) AF: 0.625 AC: 2168 AN: 3471

South Asian (SAS) AF: 0.389 AC: 1018 AN: 2619

European-Finnish (FIN) AF: 0.138 AC: 820 AN: 5926

Middle Eastern (MID) AF: 0.250 AC: 54 AN: 216

European-Non Finnish (NFE) AF: 0.162 AC: 8554 AN: 52869

Other (OTH) AF: 0.325 AC: 490 AN: 1506

Alfa AF: 0.245 Hom.: 8410

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.82
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs6521038; hg19: chrX-45632816;