chr2-74457712-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031288.4(INO80B):c.919C>T(p.Pro307Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,600,032 control chromosomes in the GnomAD database, with no homozygous occurrence. 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
Genome browser will be placed here
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.919C>T | p.Pro307Ser | missense_variant | 5/5 | ENST00000233331.12 | |
INO80B-WBP1 | NR_037849.1 | n.1013C>T | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INO80B | ENST00000233331.12 | c.919C>T | p.Pro307Ser | 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: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1447670Hom.: 0 Cov.: 33 AF XY: 0.00000694 AC XY: 5AN XY: 720662
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | The c.919C>T (p.P307S) alteration is located in exon 5 (coding exon 5) of the INO80B gene. This alteration results from a C to T substitution at nucleotide position 919, causing the proline (P) at amino acid position 307 to be replaced by a serine (S). 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