chr5-62476706-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016338.5(IPO11):c.781G>A(p.Val261Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000559 in 1,521,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016338.5 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 |
---|---|---|---|---|---|---|---|
IPO11 | NM_016338.5 | c.781G>A | p.Val261Met | missense_variant | 9/30 | ENST00000325324.11 | |
IPO11 | NM_001134779.2 | c.901G>A | p.Val301Met | missense_variant | 9/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO11 | ENST00000325324.11 | c.781G>A | p.Val261Met | missense_variant | 9/30 | 1 | NM_016338.5 | P1 | |
IPO11 | ENST00000409296.7 | c.901G>A | p.Val301Met | missense_variant | 9/30 | 2 | |||
IPO11 | ENST00000424533.5 | c.781G>A | p.Val261Met | missense_variant, NMD_transcript_variant | 9/29 | 2 | |||
IPO11 | ENST00000507640.1 | n.168+2242G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000251 AC: 5AN: 199114Hom.: 0 AF XY: 0.0000275 AC XY: 3AN XY: 109096
GnomAD4 exome AF: 0.0000569 AC: 78AN: 1369678Hom.: 0 Cov.: 29 AF XY: 0.0000530 AC XY: 36AN XY: 679186
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.901G>A (p.V301M) alteration is located in exon 9 (coding exon 9) of the IPO11 gene. This alteration results from a G to A substitution at nucleotide position 901, causing the valine (V) at amino acid position 301 to be replaced by a methionine (M). 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