2-74457854-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031288.4(INO80B):c.1061T>G(p.Leu354Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000982 in 1,558,276 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INO80B | NM_031288.4 | c.1061T>G | p.Leu354Trp | missense_variant | 5/5 | ENST00000233331.12 | |
INO80B-WBP1 | NR_037849.1 | n.1155T>G | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INO80B | ENST00000233331.12 | c.1061T>G | p.Leu354Trp | missense_variant | 5/5 | 1 | NM_031288.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152220Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000929 AC: 18AN: 193846Hom.: 0 AF XY: 0.000131 AC XY: 14AN XY: 107088
GnomAD4 exome AF: 0.000105 AC: 148AN: 1405940Hom.: 0 Cov.: 33 AF XY: 0.000106 AC XY: 74AN XY: 695936
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152336Hom.: 1 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.1061T>G (p.L354W) alteration is located in exon 5 (coding exon 5) of the INO80B gene. This alteration results from a T to G substitution at nucleotide position 1061, causing the leucine (L) at amino acid position 354 to be replaced by a tryptophan (W). 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