chr12-30631907-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BS1_Supporting
The NM_006390.4(IPO8):c.3004C>T(p.Arg1002Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,610,626 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R1002R) has been classified as Likely benign.
Frequency
Consequence
NM_006390.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO8 | NM_006390.4 | c.3004C>T | p.Arg1002Trp | missense_variant | 24/25 | ENST00000256079.9 | |
IPO8 | NM_001190995.2 | c.2389C>T | p.Arg797Trp | missense_variant | 20/21 | ||
IPO8 | XM_017018691.3 | c.2953C>T | p.Arg985Trp | missense_variant | 24/25 | ||
IPO8 | XM_017018692.2 | c.2818C>T | p.Arg940Trp | missense_variant | 23/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO8 | ENST00000256079.9 | c.3004C>T | p.Arg1002Trp | missense_variant | 24/25 | 1 | NM_006390.4 | P1 | |
IPO8 | ENST00000544829.5 | c.2389C>T | p.Arg797Trp | missense_variant | 20/21 | 2 | |||
IPO8 | ENST00000535598.1 | c.478C>T | p.Arg160Trp | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249900Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135064
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1458466Hom.: 0 Cov.: 29 AF XY: 0.0000207 AC XY: 15AN XY: 725664
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74338
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.3004C>T (p.R1002W) alteration is located in exon 24 (coding exon 24) of the IPO8 gene. This alteration results from a C to T substitution at nucleotide position 3004, causing the arginine (R) at amino acid position 1002 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