1-55283976-G-A

Variant names:

• chr1-55283976-G-A
• rs4927218
• ENST00000643232.1:n.289-39002G>A

Variant summary

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

The ENST00000643232.1(MIR4422HG):​n.289-39002G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,314 control chromosomes in the GnomAD database, including 68,888 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 0.95 (68888 hom., cov: 33)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643232.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4422HG	ENST00000643232.1		n.289-39002G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144737 AN: 152196 Hom.: 68837 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.951 AC: 144847 AN: 152314 Hom.: 68888 Cov.: 33 AF XY: 0.951 AC XY: 70814 AN XY: 74466

African (AFR) AF: 0.958 AC: 39829 AN: 41568

American (AMR) AF: 0.962 AC: 14711 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3339 AN: 3472

East Asian (EAS) AF: 0.909 AC: 4703 AN: 5176

South Asian (SAS) AF: 0.951 AC: 4591 AN: 4826

European-Finnish (FIN) AF: 0.960 AC: 10185 AN: 10614

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64287 AN: 68040

Other (OTH) AF: 0.952 AC: 2012 AN: 2114

Alfa AF: 0.945 Hom.: 15775

Bravo AF: 0.951

Asia WGS AF: 0.925 AC: 3217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.62
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs4927218; hg19: chr1-55749649;