chr15-89683706-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003847.3(PEX11A):āc.415C>Gā(p.Leu139Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003847.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX11A | NM_003847.3 | c.415C>G | p.Leu139Val | missense_variant | 3/3 | ENST00000300056.8 | |
PEX11A | NM_001271572.2 | c.322C>G | p.Leu108Val | missense_variant | 3/3 | ||
PEX11A | NM_001271573.2 | c.-21C>G | 5_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX11A | ENST00000300056.8 | c.415C>G | p.Leu139Val | missense_variant | 3/3 | 1 | NM_003847.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251346Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135842
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461502Hom.: 0 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727070
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2023 | The c.415C>G (p.L139V) alteration is located in exon 3 (coding exon 3) of the PEX11A gene. This alteration results from a C to G substitution at nucleotide position 415, causing the leucine (L) at amino acid position 139 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