NM_006390.4:c.3047G>T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_006390.4(IPO8):c.3047G>T(p.Gly1016Val) variant causes a missense change. The variant allele was found at a frequency of 0.000124 in 1,613,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006390.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IPO8 | NM_006390.4 | c.3047G>T | p.Gly1016Val | missense_variant | Exon 25 of 25 | ENST00000256079.9 | NP_006381.2 | |
IPO8 | NM_001190995.2 | c.2432G>T | p.Gly811Val | missense_variant | Exon 21 of 21 | NP_001177924.1 | ||
IPO8 | XM_017018691.3 | c.2996G>T | p.Gly999Val | missense_variant | Exon 25 of 25 | XP_016874180.1 | ||
IPO8 | XM_017018692.2 | c.2861G>T | p.Gly954Val | missense_variant | Exon 24 of 24 | XP_016874181.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IPO8 | ENST00000256079.9 | c.3047G>T | p.Gly1016Val | missense_variant | Exon 25 of 25 | 1 | NM_006390.4 | ENSP00000256079.4 | ||
IPO8 | ENST00000544829.5 | c.2432G>T | p.Gly811Val | missense_variant | Exon 21 of 21 | 2 | ENSP00000444520.1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000629 AC: 158AN: 251136Hom.: 0 AF XY: 0.000398 AC XY: 54AN XY: 135738
GnomAD4 exome AF: 0.000123 AC: 180AN: 1461304Hom.: 0 Cov.: 30 AF XY: 0.0000935 AC XY: 68AN XY: 726984
GnomAD4 genome AF: 0.000131 AC: 20AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74430
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at