1-55277426-C-G

Position:

• chr1-55277426-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR4422HG	ENST00000643232.1	n.289-45552C>G		intron_variant, non_coding_transcript_variant

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;