NM_194281.4:c.379+199T>G

Variant names:

• chr18-35479101-A-C
• rs3786394
• NM_194281.4:c.379+199T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 5 publications found

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]

ENSG00000267140 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_194281.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INO80C	NM_194281.4	MANE Select	c.379+199T>G		intron	N/A	NP_919257.2
	INO80C	NM_001098817.2		c.487+199T>G		intron	N/A	NP_001092287.1
	INO80C	NM_001308064.2		c.214+199T>G		intron	N/A	NP_001294993.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INO80C	ENST00000334598.12	TSL:1 MANE Select	c.379+199T>G		intron	N/A	ENSP00000334473.6
	ENSG00000267140	ENST00000589258.1	TSL:3	c.156+18618T>G		intron	N/A	ENSP00000467041.1
	INO80C	ENST00000283410.4	TSL:3	n.683T>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15885 AN: 152082 Hom.: 880 Cov.: 32

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.: 3 AF XY: 0.0944 AC XY: 16053 AN XY: 170076

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

GnomAD4 genome AF: 0.104 AC: 15890 AN: 152200 Hom.: 883 Cov.: 32 AF XY: 0.103 AC XY: 7632 AN XY: 74442

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: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6370 AN: 67990

Other (OTH) AF: 0.103 AC: 217 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.7
DANN	Benign	0.90
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3786394; hg19: chr18-33059065;