rs243052

Variant names:

• chr2-60363122-G-A
• rs243052
• ENST00000441598.2:n.342-3274C>T

Variant summary

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

The ENST00000441598.2(MIR4432HG):​n.342-3274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,800 control chromosomes in the GnomAD database, including 4,881 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 0.23 (4881 hom., cov: 32)
• Consequence: MIR4432HG ENST00000441598.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 9 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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
	MIR4432HG	NR_132991.1		n.342-3274C>T		intron	N/A
	MIR4432HG	NR_132992.1		n.71-3274C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR4432HG	ENST00000441598.2	TSL:3	n.342-3274C>T		intron	N/A
	MIR4432HG	ENST00000453476.1	TSL:3	n.71-3274C>T		intron	N/A
	MIR4432HG	ENST00000650395.1		n.518-3274C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34568 AN: 151682 Hom.: 4882 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.228 AC: 34580 AN: 151800 Hom.: 4881 Cov.: 32 AF XY: 0.228 AC XY: 16884 AN XY: 74176

African (AFR) AF: 0.0787 AC: 3257 AN: 41406

American (AMR) AF: 0.204 AC: 3109 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 629 AN: 3468

East Asian (EAS) AF: 0.105 AC: 541 AN: 5170

South Asian (SAS) AF: 0.111 AC: 533 AN: 4800

European-Finnish (FIN) AF: 0.413 AC: 4336 AN: 10504

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21488 AN: 67884

Other (OTH) AF: 0.200 AC: 422 AN: 2112

Alfa AF: 0.281 Hom.: 11558

Bravo AF: 0.208

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-0.16

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: rs243052;

hg19: chr2-60590257;