chr1-55246294-A-G

Variant names:

• chr1-55246294-A-G
• rs2047422
• ENST00000643232.1:n.288+28362A>G

Variant summary

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

The ENST00000643232.1(MIR4422HG):​n.288+28362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,040 control chromosomes in the GnomAD database, including 27,286 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 0.59 (27286 hom., cov: 33)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• 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 (EAS) allele frequency at 95% confidence interval = 0.735 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4422HG	ENST00000643232.1		n.288+28362A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90307 AN: 151922 Hom.: 27281 Cov.: 33

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.594 AC: 90348 AN: 152040 Hom.: 27286 Cov.: 33 AF XY: 0.594 AC XY: 44164 AN XY: 74306

African (AFR) AF: 0.504 AC: 20887 AN: 41456

American (AMR) AF: 0.698 AC: 10675 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2100 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3900 AN: 5170

South Asian (SAS) AF: 0.658 AC: 3171 AN: 4820

European-Finnish (FIN) AF: 0.514 AC: 5420 AN: 10552

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42170 AN: 67978

Other (OTH) AF: 0.625 AC: 1315 AN: 2104

Alfa AF: 0.596 Hom.: 12519

Bravo AF: 0.601

Asia WGS AF: 0.664 AC: 2310 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	2.3
DANN	Benign	0.60
PhyloP100		-0.053

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2047422;

hg19: chr1-55711967;