rs3786394

Positions:

• chr18-35479101-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
INO80C	NM_194281.4	c.379+199T>G		intron_variant		ENST00000334598.12	NP_919257.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
INO80C	ENST00000334598.12	c.379+199T>G		intron_variant		1	NM_194281.4	ENSP00000334473	P1

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

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.0779

Gnomad4 ASJ exome AF: 0.153

Gnomad4 EAS exome AF: 0.161

Gnomad4 SAS exome AF: 0.0613

Gnomad4 FIN exome AF: 0.0650

Gnomad4 NFE exome AF: 0.0935

Gnomad4 OTH exome AF: 0.101

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.0604

Gnomad4 FIN AF: 0.0543

Gnomad4 NFE AF: 0.0937

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0964 Hom.: 1117

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
DANN	Benign	0.90

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

LitVar

Other links and lift over

dbSNP: rs3786394; hg19: chr18-33059065;