rs10888912

chr1-55292134-A-G

Variant summary

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

The ENST00000643232.1(MIR4422HG):n.289-30844A>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 0.543 in 152,096 control chromosomes in the GnomAD database, including 24,686 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 0.54 (24686 hom., cov: 32)
• Consequence: MIR4422HG ENST00000643232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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 = 0.752 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.289-30844A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82536 AN: 151978 Hom.: 24680 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.543 AC: 82563 AN: 152096 Hom.: 24686 Cov.: 32 AF XY: 0.551 AC XY: 40993 AN XY: 74354

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.571

Alfa AF: 0.572 Hom.: 8263

Bravo AF: 0.525

Asia WGS AF: 0.669 AC: 2328 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	5.8
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10888912; hg19: chr1-55757807;