rs11659769

chr18-35468437-A-Gchr18-35468437-A-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

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=-0.79).
• 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/exons	MANE	UniProt
INO80C	NM_194281.4	c.*174T>C		3_prime_UTR_variant	5/5	ENST00000334598.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
INO80C	ENST00000334598.12	c.*174T>C		3_prime_UTR_variant	5/5	1	NM_194281.4	P1
INO80C	ENST00000590757.1	c.*174T>C		3_prime_UTR_variant	2/2	2
INO80C	ENST00000592173.5	c.447+9845T>C		intron_variant		2
INO80C	ENST00000441607.6			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 13957 AN: 136492 Hom.: 679 Cov.: 31

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.: 27 AF XY: 0.0808 AC XY: 50291 AN XY: 622258

Gnomad4 AFR exome AF: 0.130

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.154

Gnomad4 EAS exome AF: 0.0693

Gnomad4 SAS exome AF: 0.0532

Gnomad4 FIN exome AF: 0.0628

Gnomad4 NFE exome AF: 0.0821

Gnomad4 OTH exome AF: 0.0871

GnomAD4 genome AF: 0.102 AC: 13964 AN: 136604 Hom.: 682 Cov.: 31 AF XY: 0.102 AC XY: 6702 AN XY: 66000

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.0620

Gnomad4 NFE AF: 0.0884

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0815 Hom.: 790

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
Dann	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11659769; hg19: chr18-33048401; COSMIC: COSV58047210; COSMIC: COSV58047210;