20-13279689-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080826.2(ISM1):c.434C>T(p.Pro145Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00011 in 1,613,958 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_080826.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ISM1 | NM_080826.2 | c.434C>T | p.Pro145Leu | missense_variant | Exon 3 of 6 | ENST00000262487.5 | NP_543016.1 | |
ISM1 | XM_017027680.2 | c.434C>T | p.Pro145Leu | missense_variant | Exon 3 of 7 | XP_016883169.1 | ||
TASP1 | XR_001754319.3 | n.1369+36281G>A | intron_variant | Intron 14 of 14 | ||||
TASP1 | XR_007067463.1 | n.1370-13507G>A | intron_variant | Intron 14 of 14 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248970Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135072
GnomAD4 exome AF: 0.000113 AC: 165AN: 1461694Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 78AN XY: 727128
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.434C>T (p.P145L) alteration is located in exon 3 (coding exon 3) of the ISM1 gene. This alteration results from a C to T substitution at nucleotide position 434, causing the proline (P) at amino acid position 145 to be replaced by a leucine (L). 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