ENST00000643232.1:n.989G>A

Variant names:

• chr1-55323678-G-A
• rs17111925
• ENST00000643232.1:n.989G>A

Variant summary

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

The ENST00000643232.1(MIR4422HG):​n.989G>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 0.0448 in 153,924 control chromosomes in the GnomAD database, including 216 homozygotes. 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 0.045 (214 hom., cov: 33)
  • Exomes 𝑓: 0.046 (2 hom.)
• Consequence: MIR4422HG ENST00000643232.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

Genes affected

MIR4422HG (HGNC:53113): (MIR4422 host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.989G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6814 AN: 152184 Hom.: 215 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0462 AC: 75 AN: 1622 Hom.: 2 Cov.: 0 AF XY: 0.0471 AC XY: 44 AN XY: 934

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.0652

Gnomad4 FIN exome AF: 0.0372

Gnomad4 NFE exome AF: 0.0445

Gnomad4 OTH exome AF: 0.0429

GnomAD4 genome AF: 0.0447 AC: 6814 AN: 152302 Hom.: 214 Cov.: 33 AF XY: 0.0451 AC XY: 3362 AN XY: 74468

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0400

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0590

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0598

Gnomad4 OTH AF: 0.0517

Alfa AF: 0.0538 Hom.: 139

Bravo AF: 0.0429

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17111925; hg19: chr1-55789351;