chr18-57571588-A-G

Position:

• chr18-57571588-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP5 BP4 BA1

The NM_000140.5(FECH):​c.315-48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0671 in 1,613,854 control chromosomes in the GnomAD database, including 8,620 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.068 (820 hom., cov: 32)
  • Exomes 𝑓: 0.067 (7800 hom.)
• Consequence: FECH NM_000140.5 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:16 U:3 O:1
• Conservation: PhyloP100: 0.718

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PP5: Variant 18-57571588-A-G is Pathogenic according to our data. Variant chr18-57571588-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 562.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=11, Pathogenic_low_penetrance=1, Likely_pathogenic=2, Uncertain_significance=3, not_provided=1}. Variant chr18-57571588-A-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82). . Strength limited to SUPPORTING due to the PP5.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FECH	NM_000140.5	c.315-48T>C		intron_variant		ENST00000262093.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FECH	ENST00000262093.11	c.315-48T>C		intron_variant		1	NM_000140.5

Frequencies

GnomAD3 genomes AF: 0.0680 AC: 10341 AN: 152102 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.0190

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0969

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.0760

GnomAD3 exomes AF: 0.118 AC: 29555 AN: 250318 Hom.: 3802 AF XY: 0.107 AC XY: 14453 AN XY: 135454

Gnomad AFR exome AF: 0.0186

Gnomad AMR exome AF: 0.346

Gnomad ASJ exome AF: 0.0625

Gnomad EAS exome AF: 0.326

Gnomad SAS exome AF: 0.0892

Gnomad FIN exome AF: 0.0916

Gnomad NFE exome AF: 0.0483

Gnomad OTH exome AF: 0.0878

GnomAD4 exome AF: 0.0670 AC: 97983 AN: 1461634 Hom.: 7800 Cov.: 32 AF XY: 0.0664 AC XY: 48279 AN XY: 727128

Gnomad4 AFR exome AF: 0.0157

Gnomad4 AMR exome AF: 0.323

Gnomad4 ASJ exome AF: 0.0647

Gnomad4 EAS exome AF: 0.386

Gnomad4 SAS exome AF: 0.0887

Gnomad4 FIN exome AF: 0.0905

Gnomad4 NFE exome AF: 0.0443

Gnomad4 OTH exome AF: 0.0663

GnomAD4 genome AF: 0.0680 AC: 10351 AN: 152220 Hom.: 820 Cov.: 32 AF XY: 0.0744 AC XY: 5534 AN XY: 74406

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.0969

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0597 Hom.: 661

Bravo AF: 0.0757

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:16 Uncertain:3 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Protoporphyria, erythropoietic, 1 Pathogenic:11 Uncertain:2 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 01, 2023	Variant summary: FECH c.315-48T>C is located at a position not widely known to affect splicing. Four/four computational tools predict the variant has no significant impact on splicing, while one predicts that the variant strengthens a cryptic 3' acceptor site, located 63 nucleotides upstream from the canonical site. One publication reports experimental evidence confirming that this variant affects mRNA splicing, i.e. strengthening the activity of a cryptic splice site (a constitutive aberrant acceptor splice site), located 63 nucleotides upstream from the canonical site, thus increasing the amount of the aberrant transcripts from ~20% (normal) to ~40% (Gouya_2002). The variant allele was found at a frequency of 0.11 in 281694 control chromosomes, including 3957 homozygotes (gnomAD). In addition, this variant is reported with even higher allele frequencies in certain subpopulations, i.e. in the Latino- and East Asian subpopulations, with a frequency of frequency of 0.34 and 0.33, respectively. The observed variant frequency and the high number of homozygotes suggests that the variant is benign, even when found in homozygous state. However, this variant (c.315-48T>C) has been reported in the literature in over 95% of patients affected with Erythropoietic Protoporphyria (EPP), who were all compound heterozygotes for a pathogenic LoF variant in trans (e.g. Gouya_2002, Colombo_2013, Yasuda_2019). In addition, a mild disease phenotype with incomplete penetrance was also reported for homozygotes (e.g. Mizawa_2016). These data suggest that the pathogenicity (severity and penetrance) of the variant is genotype-dependent, i.e. largely determined by the variant observed in trans. Publications reporting experimental evidence suggest that the abnormally spliced mRNA is degraded by NMD (Gouya_2002), and FECH activity in peripheral blood lymphocytes from individuals who were homozygous for the C-allele was ~38% compared to individuals who were homozygous for the T-allele (Tahara_2010). The following publications have been ascertained in the context of this evaluation (PMID: 22591014, 16385445, 11753383, 26280465, 21132468, 30594473). Thirteen ClinVar submitters have assessed the variant since 2014: two classified the variant as uncertain significance, two as likely pathogenic, and nine as pathogenic. Based on the evidence outlined above, the variant seems to be a hypomorphic allele that is subject to interallelic interactions which might result in an incomplete penetrance, however it is considered pathogenic, when in found in trans with a LoF variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota	Aug 22, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Genomics England Pilot Project, Genomics England	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	May 21, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Dec 21, 2023	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene and is associated with erythropoietic protoporphyria 1 (MIM#177000). (I) 0106 - This gene is known to be associated with autosomal recessive disease. However, individuals with a single heterozygous FECH variant are reported to also manifest the phenotype (PMID: 20105171). (I) 0112 - Heterozygous variants in this gene have been reported to have reduced penetrance (OMIM). (I) 0210 - Splice site variant (non-canonical) proven to affect splicing of the transcript with a known effect on protein structure (intron 3 of 10). This variant was shown to cause aberrant splicing leading to a frameshift p.(Asn105Lysfs*8) that is predicted to result in nonsense-mediated decay (NMD) (PMID: 16385445; PMID: 16958804). (SP) 0251 - Variant is heterozygous. (I) 0307 - Variant is present in gnomAD >=0.05 (23726 heterozygotes, 3957 homozygotes). (SB) 0701 - Other NMD predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER, PMID: 20105171). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been previously reported as a hypomorphic allele that causes erythropoietic protoporphyria when in trans with a deleterious variant (ClinVar, PMID: 16385445; PMID: 31304091). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Studies with both homozygous and heterozygous patients show significantly reduced FECH activity compared to wild-type (PMID: 16385445; PMID: 16958804). (SP) 1101 - Very strong and specific phenotype match for this individual. (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 19, 2023	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2007	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 25, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University Hospital Muenster	Dec 08, 2021	ACMG categories: PM3,PP6,BS2 -
Uncertain significance, flagged submission	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 01, 2016	This variant was classified as: Uncertain significance. -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Jan 22, 2020	In summary, despite its frequency in the general population, this variant meets criteria to be classified as pathogenic for autosomal recessive EPP; however, it should be noted that this variant is only expected to cause disease when in compound heterozygosity with a loss-of-function allele. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	May 12, 2022	- -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 27, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 05, 2023	Observed in the apparent homozygous state in multiple individuals with an erythropoietic protoporphyria phenotype that was reported as either mild or typical and slightly increased erythrocyte-free protoporphyrin concentration or decreased FECH expression (Mizawa et al., 2016; Brancaleoni et al., 2018), but also observed in the apparent homozygous state in a few unaffected individuals from these two studies as well as in numerous individuals in large population cohorts (gnomAD); Published functional studies demonstrate abberant splicing and a mild reduction in enzyme activity (Gouya et al., 2002; Barmin-Aksozen et al., 2017); In silico analysis supports that this variant does not alter splicing; This variant is associated with the following publications: (PMID: 34758253, 21132468, 22591014, 29854403, 30712775, 32313951, 28054335, 28026050, 28093505, 31304091, 23364466, 12601550, 16385445, 18758989, 26280465, 16958804, 29941360, 11753383) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2021	- -
Pathogenic, low penetrance, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	This sequence change falls in intron 3 of the FECH gene. It does not directly change the encoded amino acid sequence of the FECH protein. This variant is present in population databases (rs2272783, gnomAD 35%), including at least one homozygous and/or hemizygous individual. This mild variant has been observed in combination with another severe FECH variant in over 90% of individuals with congenital erythropoietic porphyria (PMID: 16385445, 23364466). The vast majority of individuals that are homozygous for this variant do not have clinical symptoms, even in the presence of mild biochemical abnormalities (PMID: 11753383, 29941360). However, a few individuals with milder symptoms have been reported (PMID: 1729699, 16958804, 18758989, 26280465). ClinVar contains an entry for this variant (Variation ID: 562). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, this variant is reported to cause disease. However, as this variant is associated with a lower penetrance than other pathogenic alleles in the FECH gene, it has been classified as Pathogenic (low penetrance). -

Autosomal erythropoietic protoporphyria Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 04, 2023

The c.333-48T>C variant in FECH is a well-established pathogenic variant for erythropoietic protoporphyria (EPP; Gouya 2002 PMID: 11753383, Gouya 2006 PMID: 16385445, ClinVar Variation ID 562). This variant is found in >95% of individuals with FECH-associated EPP but has also been identified in 6.7% (10341/152102) of pan-ethnic chromosomes in gnomAD, including 817 homozygous individuals (http://gnomad.broadinstitute.org, v3.1.2). In vitro and in vivo functional studies demonstrate that the variant leads to aberrant splicing resulting in a mild but significant reduction in enzyme activity levels (Gouya 2002 PMID: 11753383, Barman-Aksözen 2017 PMID: 28093505). The majority of individuals with FECH-associated EPP carry this hypomorphic c.333-48T>C variant in compound heterozygosity with a rare loss-of-function allele, resulting in enzyme activity levels that are reduced by >70%. Most individuals who are homozygous for the c.333-48T>C variant do not exhibit any clinical symptoms despite having mild biochemical abnormalities; however, a few individuals with milder symptoms such as erythema on the face and extremities, mild photosensitivity after sun exposure have been reported (Mizawa 2016 PMID: 26280465, Alagappan 2017 PMID: 28054335), suggesting that the penetrance and disease severity associated with this variant is determined by the type of variant observed on the second copy of the FECH gene (in trans). In summary, despite its frequency in the general population, this variant is a hypomorphic allele that meets criteria to be classified as pathogenic for autosomal recessive EPP and is expected to cause more severe disease when in compound heterozygosity with a loss-of-function allele. ACMG/AMP Criteria applied: PM3_VeryStrong, PP1_Strong, PS3_Moderate. -

Jaundice;C0041834:Erythema Uncertain:1

Uncertain significance, flagged submission

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 25, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2272783; hg19: chr18-55238820;