rs10493202

Variant names:

• chr1-55298433-A-C
• rs10493202
• ENST00000643232.1:n.289-24545A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-55298433-A-C
• chr1-55298433-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643232.1(MIR4422HG):​n.289-24545A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,104 control chromosomes in the GnomAD database, including 3,323 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 0.18 (3323 hom., cov: 32)
• Consequence: MIR4422HG ENST00000643232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 2 publications found

Genes affected

MIR4422HG (HGNC:53113): (MIR4422 host gene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643232.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4422HG	ENST00000643232.1		n.289-24545A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27683 AN: 151986 Hom.: 3306 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.0814

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.182 AC: 27727 AN: 152104 Hom.: 3323 Cov.: 32 AF XY: 0.176 AC XY: 13101 AN XY: 74370

African (AFR) AF: 0.337 AC: 13966 AN: 41442

American (AMR) AF: 0.109 AC: 1659 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3472

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5172

South Asian (SAS) AF: 0.0806 AC: 389 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10602

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9420 AN: 67998

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.124 Hom.: 539

Bravo AF: 0.191

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs10493202; hg19: chr1-55764106;