chr2-60393151-T-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 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=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650395.1. 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	ENST00000650395.1		n.388+8937A>T		intron	N/A
	MIR4432HG	ENST00000730613.1		n.393+8937A>T		intron	N/A
	MIR4432HG	ENST00000730614.1		n.372+8937A>T		intron	N/A

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

African (AFR) AF: 0.108 AC: 4481 AN: 41542

American (AMR) AF: 0.155 AC: 2365 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5190

South Asian (SAS) AF: 0.117 AC: 566 AN: 4826

European-Finnish (FIN) AF: 0.310 AC: 3280 AN: 10576

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19406 AN: 67982

Other (OTH) AF: 0.170 AC: 358 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	9.9
DANN	Benign	0.84
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs243070; hg19: chr2-60620286;