chr2-216066394-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_018441.6(PECR):c.249T>C(p.Asn83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000999 in 1,613,184 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0054 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 6 hom. )
Consequence
PECR
NM_018441.6 synonymous
NM_018441.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.09
Genes affected
PECR (HGNC:18281): (peroxisomal trans-2-enoyl-CoA reductase) Enables signaling receptor binding activity and trans-2-enoyl-CoA reductase (NADPH) activity. Involved in phytol metabolic process. Located in peroxisome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 2-216066394-A-G is Benign according to our data. Variant chr2-216066394-A-G is described in ClinVar as [Benign]. Clinvar id is 709631.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.09 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00544 (829/152318) while in subpopulation AFR AF= 0.0189 (787/41572). AF 95% confidence interval is 0.0178. There are 10 homozygotes in gnomad4. There are 382 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PECR | NM_018441.6 | c.249T>C | p.Asn83= | synonymous_variant | 2/8 | ENST00000265322.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PECR | ENST00000265322.8 | c.249T>C | p.Asn83= | synonymous_variant | 2/8 | 1 | NM_018441.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00541 AC: 823AN: 152200Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00143 AC: 360AN: 251366Hom.: 1 AF XY: 0.000957 AC XY: 130AN XY: 135858
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GnomAD4 exome AF: 0.000536 AC: 783AN: 1460866Hom.: 6 Cov.: 30 AF XY: 0.000449 AC XY: 326AN XY: 726806
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at