rs243070

Variant names:

• chr2-60393151-T-A
• rs243070
• ENST00000650395.1:n.388+8937A>T

Variant summary

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

The ENST00000650395.1(MIR4432HG):​n.388+8937A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,196 control chromosomes in the GnomAD database, including 3,899 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 0.21 (3899 hom., cov: 33)
• Consequence: MIR4432HG ENST00000650395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

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=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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	ENST00000650395.1	n.388+8937A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31467 AN: 152078 Hom.: 3902 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.207 AC: 31461 AN: 152196 Hom.: 3899 Cov.: 33 AF XY: 0.202 AC XY: 15069 AN XY: 74418

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.170

Alfa AF: 0.246 Hom.: 615

Bravo AF: 0.191

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	9.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243070; hg19: chr2-60620286;