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. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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.289-24545A>C		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.0224

Gnomad4 SAS AF: 0.0806

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0790 Hom.: 101

Bravo AF: 0.191

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493202; hg19: chr1-55764106;