rs243021

Variant names:

• chr2-60357684-G-A
• rs243021
• ENST00000441598.2:n.920+1586C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-60357684-G-A
• chr2-60357684-G-C
• chr2-60357684-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000441598.2(MIR4432HG):​n.920+1586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,942 control chromosomes in the GnomAD database, including 16,130 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 0.46 (16130 hom., cov: 32)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873

Genes affected

MIR4432HG (HGNC:52005): (MIR4432 host gene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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
MIR4432HG	ENST00000441598.2	n.920+1586C>T		intron_variant	Intron 4 of 7	3

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69305 AN: 151824 Hom.: 16128 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.456 AC: 69328 AN: 151942 Hom.: 16130 Cov.: 32 AF XY: 0.458 AC XY: 34005 AN XY: 74256

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.504

Alfa AF: 0.470 Hom.: 39029

Bravo AF: 0.463

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243021; hg19: chr2-60584819;