rs17111925

Positions:

• chr1-55323678-G-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:):

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/exons	MANE	Protein	UniProt
		n.55323678G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.989G>A		non_coding_transcript_exon_variant	2/2

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;