dbSNP rs10518712: INO80:c.928-137A>G (chr15-41080041-T-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_017553.3(INO80):c.928-137A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 717,290 control chromosomes in the GnomAD database, including 1,776 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 0.074 ( 1223 hom., cov: 32)

Exomes 𝑓: 0.018 ( 553 hom. )

Consequence

INO80
NM_017553.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

Publications

3 publications found

Variant links:

Genes affected

INO80 (HGNC:26956): (INO80 complex ATPase subunit) This gene encodes a subunit of the chromatin remodeling complex, which is classified into subfamilies depending on sequence features apart from the conserved ATPase domain. This protein is the catalytic ATPase subunit of the INO80 chromatin remodeling complex, which is characterized by a DNA-binding domain. This protein is proposed to bind DNA and be recruited by the YY1 transcription factor to activate certain genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

INO80 Gene-Disease associations (from GenCC):

immunodeficiency, common variable, 1
Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

INO80 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INO80	NM_017553.3 link	c.928-137A>G		intron_variant	Intron 8 of 35	ENST00000648947.1	NP_060023.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
INO80	ENST00000648947.1 link	c.928-137A>G	intron_variant	Intron 8 of 35		NM_017553.3	ENSP00000497609.1
INO80	ENST00000558357.6 link	n.928-137A>G	intron_variant	Intron 8 of 34	1		ENSP00000453677.1
INO80	ENST00000696949.1 link	n.928-137A>G	intron_variant	Intron 8 of 33			ENSP00000512991.1

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

11242

AN:

152106

Hom.:

1211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0269

Gnomad ASJ

AF:

0.0499

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0325

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.00753

Gnomad OTH

AF:

0.0594

GnomAD4 exome

AF:

0.0184

AC:

10395

AN:

565066

Hom.:

553

AF XY:

0.0186

AC XY:

5567

AN XY:

299808

show subpopulations

African (AFR)

AF:

0.236

AC:

3662

AN:

15546

American (AMR)

AF:

0.0181

AC:

522

AN:

28870

Ashkenazi Jewish (ASJ)

AF:

0.0435

AC:

701

AN:

16106

East Asian (EAS)

AF:

0.0000306

AC:

AN:

32730

South Asian (SAS)

AF:

0.0349

AC:

1946

AN:

55716

European-Finnish (FIN)

AF:

0.000681

AC:

AN:

36728

Middle Eastern (MID)

AF:

0.0402

AC:

AN:

2240

European-Non Finnish (NFE)

AF:

0.00742

AC:

2575

AN:

347008

Other (OTH)

AF:

0.0290

AC:

873

AN:

30122

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

507

1015

1522

2030

2537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

176

264

352

440

<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:

0.0741

AC:

11286

AN:

152224

Hom.:

1223

Cov.:

AF XY:

0.0717

AC XY:

5339

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.238

AC:

9891

AN:

41514

American (AMR)

AF:

0.0269

AC:

411

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.0499

AC:

173

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.0323

AC:

156

AN:

4824

European-Finnish (FIN)

AF:

0.000188

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00754

AC:

513

AN:

68012

Other (OTH)

AF:

0.0588

AC:

124

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

440

880

1320

1760

2200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

224

336

448

560

<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:

0.0562

Hom.:

114

Bravo

AF:

0.0834

Asia WGS

AF:

0.0290

AC:

103

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.9

(source)

DANN

Benign

0.68

PhyloP100

-0.17

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