Genetic Variant MIR4432HG:n.394-23561C>G (chr2-60335579-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.283

Publications

6 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 -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	Effect	Exon rank
MIR4432HG	ENST00000730613.1 link	n.394-23561C>G	intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730614.1 link	n.373-23561C>G	intron_variant	Intron 2 of 2
MIR4432HG	ENST00000730615.1 link	n.405-23561C>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97601

AN:

151930

Hom.:

31875

Cov.:

show subpopulations

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.:

AF XY:

0.649

AC XY:

48232

AN XY:

74340

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1759

3518

5276

7035

8794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

794

1588

2382

3176

3970

<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:

0.608

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

(source)

DANN

Benign

0.49

PhyloP100

0.28

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