chr1-43949916-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_014652.4(IPO13):c.584C>T(p.Ala195Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000267 in 1,609,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014652.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO13 | NM_014652.4 | c.584C>T | p.Ala195Val | missense_variant | 2/20 | ENST00000372343.8 | |
IPO13 | XM_024451069.2 | c.-83+2232C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO13 | ENST00000372343.8 | c.584C>T | p.Ala195Val | missense_variant | 2/20 | 1 | NM_014652.4 | P1 | |
IPO13 | ENST00000489773.5 | n.116-170C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 31AN: 243960Hom.: 0 AF XY: 0.000136 AC XY: 18AN XY: 132804
GnomAD4 exome AF: 0.000282 AC: 411AN: 1457736Hom.: 0 Cov.: 35 AF XY: 0.000267 AC XY: 194AN XY: 725244
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.584C>T (p.A195V) alteration is located in exon 2 (coding exon 2) of the IPO13 gene. This alteration results from a C to T substitution at nucleotide position 584, causing the alanine (A) at amino acid position 195 to be replaced by a valine (V). 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