chr18-57580104-C-A

Position:

chr18-57580104-C-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_000140.5(FECH):c.163G>T(p.Gly55Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,613,968 control chromosomes in the GnomAD database, including 508 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G55S) has been classified as Benign.

Frequency

Genomes: 𝑓 0.020 ( 55 hom., cov: 32)

Exomes 𝑓: 0.022 ( 453 hom. )

Consequence

FECH
NM_000140.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1B:8

Conservation

PhyloP100: 0.874

Variant links:

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]

FECH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002217114).

BP6

Variant 18-57580104-C-A is Benign according to our data. Variant chr18-57580104-C-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 548.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1, Benign=4}. Variant chr18-57580104-C-A is described in Lovd as [Benign]. Variant chr18-57580104-C-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0203 (3081/152130) while in subpopulation SAS AF= 0.0512 (246/4802). AF 95% confidence interval is 0.046. There are 55 homozygotes in gnomad4. There are 1532 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 55 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FECH	NM_000140.5 linkuse as main transcript	c.163G>T	p.Gly55Cys	missense_variant	2/11	ENST00000262093.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FECH	ENST00000262093.11 linkuse as main transcript	c.163G>T	p.Gly55Cys	missense_variant	2/11	1	NM_000140.5		P22830-1

Frequencies

GnomAD3 genomes

AF:

0.0203

AC:

3083

AN:

152012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.0340

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.0154

Gnomad SAS

AF:

0.0518

Gnomad FIN

AF:

0.0176

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0211

GnomAD3 exomes

AF:

0.0221

AC:

5548

AN:

251472

Hom.:

AF XY:

0.0229

AC XY:

3112

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0157

Gnomad AMR exome

AF:

0.0269

Gnomad ASJ exome

AF:

0.00417

Gnomad EAS exome

AF:

0.0172

Gnomad SAS exome

AF:

0.0456

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0185

Gnomad OTH exome

AF:

0.0179

GnomAD4 exome

AF:

0.0218

AC:

31846

AN:

1461838

Hom.:

453

Cov.:

AF XY:

0.0224

AC XY:

16299

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.0151

Gnomad4 AMR exome

AF:

0.0271

Gnomad4 ASJ exome

AF:

0.00432

Gnomad4 EAS exome

AF:

0.0115

Gnomad4 SAS exome

AF:

0.0461

Gnomad4 FIN exome

AF:

0.0178

Gnomad4 NFE exome

AF:

0.0210

Gnomad4 OTH exome

AF:

0.0199

GnomAD4 genome

AF:

0.0203

AC:

3081

AN:

152130

Hom.:

Cov.:

AF XY:

0.0206

AC XY:

1532

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.0154

Gnomad4 AMR

AF:

0.0340

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.0155

Gnomad4 SAS

AF:

0.0512

Gnomad4 FIN

AF:

0.0176

Gnomad4 NFE

AF:

0.0183

Gnomad4 OTH

AF:

0.0204

Alfa

AF:

0.0179

Hom.:

Bravo

AF:

0.0204

TwinsUK

AF:

0.0194

AC:

ALSPAC

AF:

0.0184

AC:

ESP6500AA

AF:

0.0184

AC:

ESP6500EA

AF:

0.0183

AC:

157

ExAC

AF:

0.0222

AC:

2693

EpiCase

AF:

0.0194

EpiControl

AF:

0.0183

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:1Benign:8

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:4

Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 22, 2022	BS1 -
Likely benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	FECH: BS1, BS2 -

Protoporphyria, erythropoietic, 1

Pathogenic:1Benign:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Dec 16, 1991	- -
Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 28, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 4.7% in South Asian with 37 homozygotes -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.20

CADD

Benign

DANN

Benign

0.49

DEOGEN2

Benign

0.17

T;.;.;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.11

LIST_S2

Benign

0.66

T;T;T;.

MetaRNN

Benign

0.0022

T;T;T;T

MetaSVM

Uncertain

-0.0087

MutationAssessor

Benign

0.0

N;N;.;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.32

PROVEAN

Benign

0.56

N;N;.;.

REVEL

Uncertain

0.33

Sift

Benign

0.17

T;T;.;.

Sift4G

Uncertain

0.041

D;T;.;T

Polyphen

0.21

B;D;.;.

Vest4

0.15

MPC

0.72

ClinPred

0.0056

GERP RS

1.6

Varity_R

0.088

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over