Genetic Variant NM_194281.4:c.379+199T>G (chr18-35479101-A-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_194281.4(INO80C):c.379+199T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 476,826 control chromosomes in the GnomAD database, including 2,612 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 0.10 ( 883 hom., cov: 32)

Exomes 𝑓: 0.097 ( 1729 hom. )

Consequence

INO80C
NM_194281.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

5 publications found

Variant links:

Genes affected

INO80C (HGNC:26994): (INO80 complex subunit C) Predicted to be involved in chromatin remodeling. Part of Ino80 complex and MLL1 complex. [provided by Alliance of Genome Resources, Apr 2022]

INO80C links:

ENSG00000267140 (HGNC:):

ENSG00000267140 links:

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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=-0.51).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INO80C	NM_194281.4 link	c.379+199T>G		intron_variant	Intron 3 of 4	ENST00000334598.12	NP_919257.2	Q6PI98-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INO80C	ENST00000334598.12 link	c.379+199T>G		intron_variant	Intron 3 of 4	1	NM_194281.4	ENSP00000334473.6		Q6PI98-1
ENSG00000267140	ENST00000589258.1 link	c.156+18618T>G		intron_variant	Intron 1 of 2	3		ENSP00000467041.1		K7ENP7

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15885

AN:

152082

Hom.:

880

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0861

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.136

Gnomad SAS

AF:

0.0610

Gnomad FIN

AF:

0.0543

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0937

Gnomad OTH

AF:

0.103

GnomAD4 exome

AF:

0.0971

AC:

31535

AN:

324626

Hom.:

1729

Cov.:

AF XY:

0.0944

AC XY:

16053

AN XY:

170076

show subpopulations

African (AFR)

AF:

0.139

AC:

1191

AN:

8544

American (AMR)

AF:

0.0779

AC:

815

AN:

10460

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

1637

AN:

10680

East Asian (EAS)

AF:

0.161

AC:

3829

AN:

23732

South Asian (SAS)

AF:

0.0613

AC:

1510

AN:

24646

European-Finnish (FIN)

AF:

0.0650

AC:

1501

AN:

23080

Middle Eastern (MID)

AF:

0.0976

AC:

177

AN:

1814

European-Non Finnish (NFE)

AF:

0.0935

AC:

18877

AN:

201808

Other (OTH)

AF:

0.101

AC:

1998

AN:

19862

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1321

2642

3963

5284

6605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

252

378

504

630

<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:

0.104

AC:

15890

AN:

152200

Hom.:

883

Cov.:

AF XY:

0.103

AC XY:

7632

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.139

AC:

5766

AN:

41502

American (AMR)

AF:

0.0861

AC:

1317

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

551

AN:

3470

East Asian (EAS)

AF:

0.135

AC:

702

AN:

5182

South Asian (SAS)

AF:

0.0604

AC:

292

AN:

4832

European-Finnish (FIN)

AF:

0.0543

AC:

576

AN:

10614

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0937

AC:

6370

AN:

67990

Other (OTH)

AF:

0.103

AC:

217

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

750

1499

2249

2998

3748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.0999

Hom.:

2799

Bravo

AF:

0.110

Asia WGS

AF:

0.0870

AC:

302

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.7

(source)

DANN

Benign

0.90

PhyloP100

-0.11

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