chr18-57545084-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000140.5(FECH):c.*5628C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,964 control chromosomes in the GnomAD database, including 10,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.33 ( 10054 hom., cov: 32)
Consequence
FECH
NM_000140.5 3_prime_UTR
NM_000140.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.80
Genes affected
FECH (HGNC:3647): (ferrochelatase) The protein encoded by this gene is localized to the mitochondrion, where it catalyzes the insertion of the ferrous form of iron into protoporphyrin IX in the heme synthesis pathway. Mutations in this gene are associated with erythropoietic protoporphyria. Two transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome 3.[provided by RefSeq, May 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=-0.9).
BP6
Variant 18-57545084-G-T is Benign according to our data. Variant chr18-57545084-G-T is described in ClinVar as [Benign]. Clinvar id is 327316.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FECH | NM_000140.5 | c.*5628C>A | 3_prime_UTR_variant | 11/11 | ENST00000262093.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FECH | ENST00000262093.11 | c.*5628C>A | 3_prime_UTR_variant | 11/11 | 1 | NM_000140.5 | |||
FECH | ENST00000652755.1 | c.*5628C>A | 3_prime_UTR_variant | 11/11 |
Frequencies
GnomAD3 genomes AF: 0.327 AC: 49684AN: 151846Hom.: 10055 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.327 AC: 49674AN: 151964Hom.: 10054 Cov.: 32 AF XY: 0.319 AC XY: 23659AN XY: 74252
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Protoporphyria, erythropoietic, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at