rs2047422

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-55246294-A-G
• chr1-55246294-A-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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.288+28362A>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.504

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.625

Alfa AF: 0.595 Hom.: 10963

Bravo AF: 0.601

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047422; hg19: chr1-55711967;