1-145912191-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003846.3(PEX11B):āc.750A>Gā(p.Leu250Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,902 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 Likely benign (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
PEX11B
NM_003846.3 synonymous
NM_003846.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
Genes affected
PEX11B (HGNC:8853): (peroxisomal biogenesis factor 11 beta) The protein encoded by this gene facilitates peroxisomal proliferation and interacts with PEX19. The encoded protein is found in the peroxisomal membrane. Several transcript variants, some protein-coding and some not protein-coding, have been found for this gene. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 1-145912191-T-C is Benign according to our data. Variant chr1-145912191-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1603976.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.35 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PEX11B | NM_003846.3 | c.750A>G | p.Leu250Leu | synonymous_variant | 4/4 | ENST00000369306.8 | NP_003837.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PEX11B | ENST00000369306.8 | c.750A>G | p.Leu250Leu | synonymous_variant | 4/4 | 1 | NM_003846.3 | ENSP00000358312.3 | ||
| PEX11B | ENST00000537888.1 | c.708A>G | p.Leu236Leu | synonymous_variant | 4/4 | 2 | ENSP00000437510.1 | |||
| PEX11B | ENST00000428634.1 | c.216A>G | p.Leu72Leu | synonymous_variant | 1/2 | 2 | ENSP00000414018.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248822Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134492
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GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459902Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726188
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GnomAD4 genome
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 23, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at