NM_194281.4:c.447+3101A>G

Variant names:

• chr18-35475181-T-C
• rs9964280
• NM_194281.4:c.447+3101A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_194281.4(INO80C):​c.447+3101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0737 in 152,100 control chromosomes in the GnomAD database, including 1,278 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 (1278 hom., cov: 32)
• Consequence: INO80C NM_194281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INO80C	NM_194281.4	c.447+3101A>G		intron_variant	Intron 4 of 4	ENST00000334598.12	NP_919257.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INO80C	ENST00000334598.12	c.447+3101A>G		intron_variant	Intron 4 of 4	1	NM_194281.4	ENSP00000334473.6
ENSG00000267140	ENST00000589258.1	c.156+22538A>G		intron_variant	Intron 1 of 2	3		ENSP00000467041.1

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11185 AN: 151982 Hom.: 1274 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00272

Gnomad OTH AF: 0.0586

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0737 AC: 11214 AN: 152100 Hom.: 1278 Cov.: 32 AF XY: 0.0743 AC XY: 5523 AN XY: 74362

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0452

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.0793

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.00272

Gnomad4 OTH AF: 0.0599

Alfa AF: 0.0288 Hom.: 133

Bravo AF: 0.0816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.7
DANN	Benign	0.86

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs9964280; hg19: chr18-33055145;