12-38318448-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001013620.4(ALG10B):c.359C>T(p.Pro120Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,461,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001013620.4 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 |
---|---|---|---|---|---|---|---|---|
ALG10B | NM_001013620.4 | c.359C>T | p.Pro120Leu | missense_variant | Exon 2 of 3 | ENST00000308742.9 | NP_001013642.2 | |
ALG10B | NM_001308340.2 | c.359C>T | p.Pro120Leu | missense_variant | Exon 2 of 3 | NP_001295269.2 | ||
ALG10B | XM_005268665.5 | c.179C>T | p.Pro60Leu | missense_variant | Exon 2 of 3 | XP_005268722.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251360Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135866
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461764Hom.: 0 Cov.: 36 AF XY: 0.0000179 AC XY: 13AN XY: 727180
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.359C>T (p.P120L) alteration is located in exon 2 (coding exon 2) of the ALG10B gene. This alteration results from a C to T substitution at nucleotide position 359, causing the proline (P) at amino acid position 120 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