rs7050391

Variant names:

• chrX-45745845-C-T
• rs7050391
• ENST00000602461.1:n.745G>A

Variant summary

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

The ENST00000602461.1(MIR222HG):​n.745G>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 ENST00000602461.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 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 (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 rank	MANE	Protein	UniProt
MIR222HG	NR_170290.1	n.24291G>A		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.745G>A		non_coding_transcript_exon_variant	Exon 2 of 2	5
MIR222HG	ENST00000688264.3	n.1759G>A		non_coding_transcript_exon_variant	Exon 4 of 4
MIR222HG	ENST00000780202.1	n.746G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0178 AC: 1993 AN: 111659 Hom.: 43 Cov.: 22

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

African (AFR) AF: 0.0511 AC: 7 AN: 137

American (AMR) AF: 0.00 AC: 0 AN: 379

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 87

East Asian (EAS) AF: 0.00 AC: 0 AN: 241

South Asian (SAS) AF: 0.00 AC: 0 AN: 390

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 65

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.000503 AC: 1 AN: 1990

Other (OTH) AF: 0.00901 AC: 1 AN: 111

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

African (AFR) AF: 0.0595 AC: 1826 AN: 30695

American (AMR) AF: 0.0121 AC: 128 AN: 10537

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2647

East Asian (EAS) AF: 0.000281 AC: 1 AN: 3565

South Asian (SAS) AF: 0.00150 AC: 4 AN: 2675

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6043

Middle Eastern (MID) AF: 0.00461 AC: 1 AN: 217

European-Non Finnish (NFE) AF: 0.000264 AC: 14 AN: 53116

Other (OTH) AF: 0.0157 AC: 24 AN: 1532

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7050391; hg19: chrX-45605273;