12-30631984-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006390.4(IPO8):c.2927A>T(p.Tyr976Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,546 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006390.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IPO8 | NM_006390.4 | c.2927A>T | p.Tyr976Phe | missense_variant | Exon 24 of 25 | ENST00000256079.9 | NP_006381.2 | |
IPO8 | NM_001190995.2 | c.2312A>T | p.Tyr771Phe | missense_variant | Exon 20 of 21 | NP_001177924.1 | ||
IPO8 | XM_017018691.3 | c.2876A>T | p.Tyr959Phe | missense_variant | Exon 24 of 25 | XP_016874180.1 | ||
IPO8 | XM_017018692.2 | c.2741A>T | p.Tyr914Phe | missense_variant | Exon 23 of 24 | XP_016874181.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IPO8 | ENST00000256079.9 | c.2927A>T | p.Tyr976Phe | missense_variant | Exon 24 of 25 | 1 | NM_006390.4 | ENSP00000256079.4 | ||
IPO8 | ENST00000544829.5 | c.2312A>T | p.Tyr771Phe | missense_variant | Exon 20 of 21 | 2 | ENSP00000444520.1 | |||
IPO8 | ENST00000535598.1 | c.398A>T | p.Tyr133Phe | missense_variant | Exon 3 of 3 | 3 | ENSP00000446232.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250120Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135164
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460372Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726530
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2927A>T (p.Y976F) alteration is located in exon 24 (coding exon 24) of the IPO8 gene. This alteration results from a A to T substitution at nucleotide position 2927, causing the tyrosine (Y) at amino acid position 976 to be replaced by a phenylalanine (F). 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