chr18-57546149-C-A

Position:

• chr18-57546149-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000140.5(FECH):​c.*4563G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 152,132 control chromosomes in the GnomAD database, including 47,363 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.77 (47363 hom., cov: 32)
• Consequence: FECH NM_000140.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.552

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 18-57546149-C-A is Benign according to our data. Variant chr18-57546149-C-A is described in ClinVar as [Benign]. Clinvar id is 327335.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FECH	NM_000140.5	c.*4563G>T		3_prime_UTR_variant	11/11	ENST00000262093.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FECH	ENST00000262093.11	c.*4563G>T		3_prime_UTR_variant	11/11	1	NM_000140.5
FECH	ENST00000652755.1	c.*4563G>T		3_prime_UTR_variant	11/11

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117624 AN: 152014 Hom.: 47356 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.805

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.773 AC: 117666 AN: 152132 Hom.: 47363 Cov.: 32 AF XY: 0.778 AC XY: 57846 AN XY: 74374

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.806

Alfa AF: 0.853 Hom.: 75550

Bravo AF: 0.755

Asia WGS AF: 0.857 AC: 2977 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Protoporphyria, erythropoietic, 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs663774; hg19: chr18-55213381;