12-30631990-G-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_006390.4(IPO8):c.2921C>A(p.Ala974Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,612,310 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 Uncertain significance (★).
Frequency
Consequence
NM_006390.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IPO8 | NM_006390.4 | c.2921C>A | p.Ala974Asp | missense_variant | Exon 24 of 25 | ENST00000256079.9 | NP_006381.2 | |
IPO8 | NM_001190995.2 | c.2306C>A | p.Ala769Asp | missense_variant | Exon 20 of 21 | NP_001177924.1 | ||
IPO8 | XM_017018691.3 | c.2870C>A | p.Ala957Asp | missense_variant | Exon 24 of 25 | XP_016874180.1 | ||
IPO8 | XM_017018692.2 | c.2735C>A | p.Ala912Asp | 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.2921C>A | p.Ala974Asp | missense_variant | Exon 24 of 25 | 1 | NM_006390.4 | ENSP00000256079.4 | ||
IPO8 | ENST00000544829.5 | c.2306C>A | p.Ala769Asp | missense_variant | Exon 20 of 21 | 2 | ENSP00000444520.1 | |||
IPO8 | ENST00000535598.1 | c.392C>A | p.Ala131Asp | missense_variant | Exon 3 of 3 | 3 | ENSP00000446232.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000920 AC: 23AN: 249894Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135062
GnomAD4 exome AF: 0.0000473 AC: 69AN: 1460030Hom.: 0 Cov.: 30 AF XY: 0.0000537 AC XY: 39AN XY: 726346
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74462
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2921C>A (p.A974D) alteration is located in exon 24 (coding exon 24) of the IPO8 gene. This alteration results from a C to A substitution at nucleotide position 2921, causing the alanine (A) at amino acid position 974 to be replaced by an aspartic acid (D). 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