18-35468437-A-T

Variant names:

• chr18-35468437-A-T
• rs11659769
• NM_194281.4:c.*174T>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_194281.4(INO80C):​c.*174T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000352 in 1,418,536 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000022 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000037 (0 hom.)
• Consequence: INO80C NM_194281.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 6 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

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.*174T>A		3_prime_UTR	Exon 5 of 5	NP_919257.2
	INO80C	NM_001098817.2		c.*174T>A		3_prime_UTR	Exon 7 of 7	NP_001092287.1
	INO80C	NM_001308064.2		c.*174T>A		3_prime_UTR	Exon 5 of 5	NP_001294993.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	INO80C	ENST00000334598.12	TSL:1 MANE Select	c.*174T>A		3_prime_UTR	Exon 5 of 5	ENSP00000334473.6
	ENSG00000267140	ENST00000589258.1	TSL:3	c.157-21482T>A		intron	N/A	ENSP00000467041.1
	INO80C	ENST00000590757.1	TSL:2	c.*174T>A		3_prime_UTR	Exon 2 of 2	ENSP00000467708.1

Frequencies

GnomAD3 genomes AF: 0.0000220 AC: 3 AN: 136562 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000602

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000367 AC: 47 AN: 1281974 Hom.: 0 Cov.: 27 AF XY: 0.0000369 AC XY: 23 AN XY: 622586

African (AFR) AF: 0.00 AC: 0 AN: 28722

American (AMR) AF: 0.00 AC: 0 AN: 20898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18454

East Asian (EAS) AF: 0.00125 AC: 45 AN: 36100

South Asian (SAS) AF: 0.00 AC: 0 AN: 60790

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31852

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3534

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1028614

Other (OTH) AF: 0.0000377 AC: 2 AN: 53010

GnomAD4 genome AF: 0.0000220 AC: 3 AN: 136562 Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 2 AN XY: 65926

African (AFR) AF: 0.00 AC: 0 AN: 34524

American (AMR) AF: 0.00 AC: 0 AN: 13344

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3344

East Asian (EAS) AF: 0.000602 AC: 3 AN: 4984

South Asian (SAS) AF: 0.00 AC: 0 AN: 4034

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8906

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 304

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64388

Other (OTH) AF: 0.00 AC: 0 AN: 1862

Alfa AF: 0.00 Hom.: 1138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		1.4
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

Other links and lift over

dbSNP: rs11659769; hg19: chr18-33048401;