15-89683398-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003847.3(PEX11A):c.723G>C(p.Gln241His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,124 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_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.723G>C | p.Gln241His | missense_variant | 3/3 | ENST00000300056.8 | |
PEX11A | NM_001271572.2 | c.630G>C | p.Gln210His | missense_variant | 3/3 | ||
PEX11A | NM_001271573.2 | c.288G>C | p.Gln96His | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX11A | ENST00000300056.8 | c.723G>C | p.Gln241His | missense_variant | 3/3 | 1 | NM_003847.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250142Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135078
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460952Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726706
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | The c.723G>C (p.Q241H) alteration is located in exon 3 (coding exon 3) of the PEX11A gene. This alteration results from a G to C substitution at nucleotide position 723, causing the glutamine (Q) at amino acid position 241 to be replaced by a histidine (H). 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