ENST00000730613.1:n.394-23561C>G

Variant names:

• chr2-60335579-G-C
• rs9784100
• ENST00000730613.1:n.394-23561C>G

Variant summary

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

The ENST00000730613.1(MIR4432HG):​n.394-23561C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,048 control chromosomes in the GnomAD database, including 31,925 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 0.64 (31925 hom., cov: 32)
• Consequence: MIR4432HG ENST00000730613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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	ENST00000730613.1	n.394-23561C>G		intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730614.1	n.373-23561C>G		intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730615.1	n.405-23561C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97601 AN: 151930 Hom.: 31875 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.643 AC: 97708 AN: 152048 Hom.: 31925 Cov.: 32 AF XY: 0.649 AC XY: 48232 AN XY: 74340

African (AFR) AF: 0.751 AC: 31160 AN: 41502

American (AMR) AF: 0.632 AC: 9661 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4202 AN: 5172

South Asian (SAS) AF: 0.705 AC: 3394 AN: 4814

European-Finnish (FIN) AF: 0.644 AC: 6793 AN: 10554

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38902 AN: 67942

Other (OTH) AF: 0.622 AC: 1317 AN: 2116

Alfa AF: 0.608 Hom.: 3489

Bravo AF: 0.644

Asia WGS AF: 0.769 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.49
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs9784100; hg19: chr2-60562714;