dbSNP rs1055271: MIOX:c.*55G>C (chr22-50489911-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 NM_017584.6(MIOX):c.*55G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,534,558 control chromosomes in the GnomAD database, including 88,026 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 0.27 ( 6423 hom., cov: 34)

Exomes 𝑓: 0.34 ( 81603 hom. )

Consequence

MIOX
NM_017584.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

6 publications found

Variant links:

Genes affected

MIOX (HGNC:14522): (myo-inositol oxygenase) Enables ferric iron binding activity and inositol oxygenase activity. Involved in inositol catabolic process. Predicted to be located in cytoplasm and inclusion body. [provided by Alliance of Genome Resources, Apr 2022]

MIOX 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIOX	NM_017584.6 link	c.*55G>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000216075.11	NP_060054.4
MIOX	XM_005261925.5 link	c.*55G>C		3_prime_UTR_variant	Exon 9 of 9		XP_005261982.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
MIOX	ENST00000216075.11 link	c.*55G>C	3_prime_UTR_variant	Exon 10 of 10	1	NM_017584.6	ENSP00000216075.6
MIOX	ENST00000395732.7 link	c.*86G>C	3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000379081.3
MIOX	ENST00000395733.7 link	c.*86G>C	3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000379082.3
MIOX	ENST00000451761.1 link	c.*55G>C	3_prime_UTR_variant	Exon 9 of 9	3		ENSP00000409894.1

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40990

AN:

152090

Hom.:

6423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.301

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.354

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.339

AC:

469258

AN:

1382350

Hom.:

81603

Cov.:

AF XY:

0.337

AC XY:

232940

AN XY:

691304

show subpopulations

African (AFR)

AF:

0.110

AC:

3527

AN:

31926

American (AMR)

AF:

0.315

AC:

13906

AN:

44168

Ashkenazi Jewish (ASJ)

AF:

0.343

AC:

8782

AN:

25612

East Asian (EAS)

AF:

0.348

AC:

13670

AN:

39238

South Asian (SAS)

AF:

0.242

AC:

20523

AN:

84730

European-Finnish (FIN)

AF:

0.281

AC:

12286

AN:

43768

Middle Eastern (MID)

AF:

0.361

AC:

1453

AN:

4026

European-Non Finnish (NFE)

AF:

0.358

AC:

376368

AN:

1051070

Other (OTH)

AF:

0.324

AC:

18743

AN:

57812

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

15675

31350

47024

62699

78374

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11608

23216

34824

46432

58040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.269

AC:

40990

AN:

152208

Hom.:

6423

Cov.:

AF XY:

0.264

AC XY:

19650

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.117

AC:

4849

AN:

41548

American (AMR)

AF:

0.283

AC:

4333

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.342

AC:

1185

AN:

3468

East Asian (EAS)

AF:

0.326

AC:

1688

AN:

5180

South Asian (SAS)

AF:

0.229

AC:

1103

AN:

4820

European-Finnish (FIN)

AF:

0.265

AC:

2806

AN:

10604

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.354

AC:

24055

AN:

67970

Other (OTH)

AF:

0.290

AC:

612

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1553

3107

4660

6214

7767

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.214

Hom.:

571

Bravo

AF:

0.271

Asia WGS

AF:

0.240

AC:

835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.1

(source)

DANN

Benign

0.32

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over