chr2-74457695-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031288.4(INO80B):c.902C>G(p.Ser301Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,599,250 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031288.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INO80B | NM_031288.4 | c.902C>G | p.Ser301Cys | missense_variant | 5/5 | ENST00000233331.12 | |
INO80B-WBP1 | NR_037849.1 | n.996C>G | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INO80B | ENST00000233331.12 | c.902C>G | p.Ser301Cys | missense_variant | 5/5 | 1 | NM_031288.4 | P1 | |
INO80B | ENST00000409917.5 | downstream_gene_variant | 2 | ||||||
INO80B | ENST00000469849.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000173 AC: 39AN: 225600Hom.: 1 AF XY: 0.000272 AC XY: 34AN XY: 125134
GnomAD4 exome AF: 0.0000670 AC: 97AN: 1446870Hom.: 1 Cov.: 33 AF XY: 0.000108 AC XY: 78AN XY: 720172
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152380Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.902C>G (p.S301C) alteration is located in exon 5 (coding exon 5) of the INO80B gene. This alteration results from a C to G substitution at nucleotide position 902, causing the serine (S) at amino acid position 301 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at