chr1-45012132-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000652165.1(UROD):c.-136+47T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00725 in 1,316,932 control chromosomes in the GnomAD database, including 487 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.034 ( 264 hom., cov: 32)
Exomes 𝑓: 0.0038 ( 223 hom. )
Consequence
UROD
ENST00000652165.1 intron
ENST00000652165.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.61
Genes affected
UROD (HGNC:12591): (uroporphyrinogen decarboxylase) This gene encodes an enzyme in the heme biosynthetic pathway. This enzyme is responsible for catalyzing the conversion of uroporphyrinogen to coproporphyrinogen through the removal of four carboxymethyl side chains. Mutations and deficiency in this enzyme are known to cause familial porphyria cutanea tarda and hepatoerythropoetic porphyria.[provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 1-45012132-T-G is Benign according to our data. Variant chr1-45012132-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 368874.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UROD | ENST00000650713.1 | c.-86+47T>G | intron_variant | ||||||
UROD | ENST00000652165.1 | c.-136+47T>G | intron_variant | ||||||
UROD | ENST00000651476.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0336 AC: 5101AN: 152040Hom.: 262 Cov.: 32
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GnomAD3 exomes AF: 0.00857 AC: 2010AN: 234542Hom.: 118 AF XY: 0.00621 AC XY: 790AN XY: 127114
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GnomAD4 exome AF: 0.00380 AC: 4430AN: 1164774Hom.: 223 Cov.: 16 AF XY: 0.00327 AC XY: 1934AN XY: 592316
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GnomAD4 genome AF: 0.0336 AC: 5114AN: 152158Hom.: 264 Cov.: 32 AF XY: 0.0324 AC XY: 2411AN XY: 74406
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Porphyria cutanea tarda Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at