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. The variant received -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
• Publications: 136 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441598.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.920+1586C>T		intron	N/A
	MIR4432HG	ENST00000730613.1		n.393+44404C>T		intron	N/A
	MIR4432HG	ENST00000730614.1		n.372+44404C>T		intron	N/A

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

African (AFR) AF: 0.373 AC: 15457 AN: 41420

American (AMR) AF: 0.550 AC: 8412 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1905 AN: 3466

East Asian (EAS) AF: 0.667 AC: 3456 AN: 5182

South Asian (SAS) AF: 0.496 AC: 2391 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4584 AN: 10518

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31541 AN: 67930

Other (OTH) AF: 0.504 AC: 1067 AN: 2116

Alfa AF: 0.467 Hom.: 79285

Bravo AF: 0.463

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	17
DANN	Benign	0.75
PhyloP100		0.87

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs243021;

hg19: chr2-60584819;