1-55277426-C-G

Variant names:

• chr1-55277426-C-G
• rs2047418
• ENST00000643232.1:n.289-45552C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643232.1(MIR4422HG):​n.289-45552C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,002 control chromosomes in the GnomAD database, including 45,916 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 0.78 (45916 hom., cov: 31)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.884 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.289-45552C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117879 AN: 151884 Hom.: 45892 Cov.: 31

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.906

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.776 AC: 117956 AN: 152002 Hom.: 45916 Cov.: 31 AF XY: 0.777 AC XY: 57729 AN XY: 74300

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.775

Alfa AF: 0.714 Hom.: 2132

Bravo AF: 0.780

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047418; hg19: chr1-55743099;