chrX-45745845-C-T

Position:

• chrX-45745845-C-T

Variant summary

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

The NR_170290.1(MIR222HG):​n.24291G>A 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 0.0174 in 115,116 control chromosomes in the GnomAD database, including 43 homozygotes. There are 557 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 0.018 (43 hom., 557 hem., cov: 22)
  • Exomes 𝑓: 0.0026 (0 hom. 0 hem.)
• Consequence: MIR222HG NR_170290.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR222HG	NR_170290.1	n.24291G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR222HG	ENST00000602461.1	n.745G>A		non_coding_transcript_exon_variant	2/2	5
MIR222HG	ENST00000688264.2	n.336G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0178 AC: 1993 AN: 111659 Hom.: 43 Cov.: 22 AF XY: 0.0163 AC XY: 552 AN XY: 33857

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0122

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000280

Gnomad SAS AF: 0.00149

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.000264

Gnomad OTH AF: 0.0159

GnomAD4 exome AF: 0.00265 AC: 9 AN: 3402 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 760

Gnomad4 AFR exome AF: 0.0511

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000503

Gnomad4 OTH exome AF: 0.00901

GnomAD4 genome AF: 0.0179 AC: 1998 AN: 111714 Hom.: 43 Cov.: 22 AF XY: 0.0164 AC XY: 557 AN XY: 33922

Gnomad4 AFR AF: 0.0595

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000281

Gnomad4 SAS AF: 0.00150

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000264

Gnomad4 OTH AF: 0.0157

Alfa AF: 0.0134 Hom.: 29

Bravo AF: 0.0211

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.14
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7050391; hg19: chrX-45605273;