Genetic Variant MIR4432HG:n.388+8937A>T (chr2-60393151-T-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

Publications

23 publications found

Variant links:

Genes affected

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

MIR4432HG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR4432HG	ENST00000650395.1 link	n.388+8937A>T	intron_variant	Intron 2 of 3
MIR4432HG	ENST00000730613.1 link	n.393+8937A>T	intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730614.1 link	n.372+8937A>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31467

AN:

152078

Hom.:

3902

Cov.:

show subpopulations

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.:

AF XY:

0.202

AC XY:

15069

AN XY:

74418

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.285

AC:

19406

AN:

67982

Other (OTH)

AF:

0.170

AC:

358

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1250

2501

3751

5002

6252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

330

660

990

1320

1650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.84

PhyloP100

0.13

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over