ENST00000441598.2:n.94-816G>A

Variant names:

• chr2-60379436-C-T
• rs243030
• ENST00000441598.2:n.94-816G>A

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.94-816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,862 control chromosomes in the GnomAD database, including 8,811 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 0.33 (8811 hom., cov: 31)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	NR_132991.1		n.94-816G>A		intron	N/A
	MIR4432HG	NR_132992.1		n.70+11870G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.94-816G>A		intron	N/A
	MIR4432HG	ENST00000453476.1	TSL:3	n.70+11870G>A		intron	N/A
	MIR4432HG	ENST00000650395.1		n.389-9399G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49636 AN: 151744 Hom.: 8812 Cov.: 31

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.00596

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.327 AC: 49650 AN: 151862 Hom.: 8811 Cov.: 31 AF XY: 0.318 AC XY: 23559 AN XY: 74188

African (AFR) AF: 0.290 AC: 12011 AN: 41374

American (AMR) AF: 0.244 AC: 3721 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3470

East Asian (EAS) AF: 0.00617 AC: 32 AN: 5188

South Asian (SAS) AF: 0.155 AC: 745 AN: 4808

European-Finnish (FIN) AF: 0.394 AC: 4136 AN: 10486

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26963 AN: 67964

Other (OTH) AF: 0.288 AC: 608 AN: 2112

Alfa AF: 0.346 Hom.: 3580

Bravo AF: 0.314

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.60
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs243030; hg19: chr2-60606571;