dbSNP rs11659769: INO80C:c.*174T>C (chr18-35468437-A-G) – 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.*174T>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 0.0839 in 1,417,912 control chromosomes in the GnomAD database, including 5,288 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 ( 682 hom., cov: 31)

Exomes 𝑓: 0.082 ( 4606 hom. )

Consequence

INO80C
NM_194281.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.39

Publications

6 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:

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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INO80C	NM_194281.4 link	c.*174T>C		3_prime_UTR_variant	Exon 5 of 5	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.*174T>C		3_prime_UTR_variant	Exon 5 of 5	1	NM_194281.4	ENSP00000334473.6		Q6PI98-1
ENSG00000267140	ENST00000589258.1 link	c.157-21482T>C		intron_variant	Intron 1 of 2	3		ENSP00000467041.1		K7ENP7

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

13957

AN:

136492

Hom.:

679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.0906

Gnomad AMR

AF:

0.0820

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.0811

Gnomad SAS

AF:

0.0693

Gnomad FIN

AF:

0.0620

Gnomad MID

AF:

0.0691

Gnomad NFE

AF:

0.0884

Gnomad OTH

AF:

0.106

GnomAD4 exome

AF:

0.0820

AC:

105028

AN:

1281308

Hom.:

4606

Cov.:

AF XY:

0.0808

AC XY:

50291

AN XY:

622258

show subpopulations

African (AFR)

AF:

0.130

AC:

3734

AN:

28692

American (AMR)

AF:

0.0661

AC:

1381

AN:

20892

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

2848

AN:

18438

East Asian (EAS)

AF:

0.0693

AC:

2501

AN:

36066

South Asian (SAS)

AF:

0.0532

AC:

3236

AN:

60770

European-Finnish (FIN)

AF:

0.0628

AC:

1999

AN:

31830

Middle Eastern (MID)

AF:

0.0943

AC:

333

AN:

3530

European-Non Finnish (NFE)

AF:

0.0821

AC:

84383

AN:

1028112

Other (OTH)

AF:

0.0871

AC:

4613

AN:

52978

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

4259

8518

12776

17035

21294

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3388

6776

10164

13552

16940

<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:

0.102

AC:

13964

AN:

136604

Hom.:

682

Cov.:

AF XY:

0.102

AC XY:

6702

AN XY:

66000

show subpopulations

African (AFR)

AF:

0.147

AC:

5102

AN:

34610

American (AMR)

AF:

0.0820

AC:

1095

AN:

13356

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

549

AN:

3340

East Asian (EAS)

AF:

0.0811

AC:

403

AN:

4970

South Asian (SAS)

AF:

0.0686

AC:

276

AN:

4024

European-Finnish (FIN)

AF:

0.0620

AC:

552

AN:

8904

Middle Eastern (MID)

AF:

0.0709

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.0884

AC:

5689

AN:

64364

Other (OTH)

AF:

0.106

AC:

199

AN:

1882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

620

1239

1859

2478

3098

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0839

Hom.:

1138

Bravo

AF:

0.0968

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

9.7

(source)

DANN

Benign

0.79

PhyloP100

1.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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