rs2047422

chr1-55246294-A-Gchr1-55246294-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.288+28362A>G		intron_variant, non_coding_transcript_variant

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;