chr15-89683874-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003847.3(PEX11A):c.247C>T(p.Arg83Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000534 in 1,613,780 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX11A | NM_003847.3 | c.247C>T | p.Arg83Cys | missense_variant | 3/3 | ENST00000300056.8 | |
PEX11A | NM_001271573.2 | c.-189C>T | 5_prime_UTR_variant | 2/2 | |||
PEX11A | NM_001271572.2 | c.173-19C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX11A | ENST00000300056.8 | c.247C>T | p.Arg83Cys | missense_variant | 3/3 | 1 | NM_003847.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000239 AC: 60AN: 251434Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135886
GnomAD4 exome AF: 0.000560 AC: 819AN: 1461578Hom.: 3 Cov.: 32 AF XY: 0.000513 AC XY: 373AN XY: 727138
GnomAD4 genome AF: 0.000276 AC: 42AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.247C>T (p.R83C) alteration is located in exon 3 (coding exon 3) of the PEX11A gene. This alteration results from a C to T substitution at nucleotide position 247, causing the arginine (R) at amino acid position 83 to be replaced by a cysteine (C). 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