chr18-57545826-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000140.5(FECH):​c.*4886T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,012 control chromosomes in the GnomAD database, including 5,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5767 hom., cov: 32)

Consequence

FECH
NM_000140.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.178
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 18-57545826-A-C is Benign according to our data. Variant chr18-57545826-A-C is described in ClinVar as [Benign]. Clinvar id is 327328.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FECHNM_000140.5 linkuse as main transcriptc.*4886T>G 3_prime_UTR_variant 11/11 ENST00000262093.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FECHENST00000262093.11 linkuse as main transcriptc.*4886T>G 3_prime_UTR_variant 11/111 NM_000140.5 P22830-1
FECHENST00000652755.1 linkuse as main transcriptc.*4886T>G 3_prime_UTR_variant 11/11 P22830-2

Frequencies

GnomAD3 genomes
AF:
0.264
AC:
40156
AN:
151894
Hom.:
5771
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.284
Gnomad AMI
AF:
0.285
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.00309
Gnomad SAS
AF:
0.138
Gnomad FIN
AF:
0.195
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.257
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
40153
AN:
152012
Hom.:
5767
Cov.:
32
AF XY:
0.255
AC XY:
18931
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.284
Gnomad4 AMR
AF:
0.213
Gnomad4 ASJ
AF:
0.352
Gnomad4 EAS
AF:
0.00310
Gnomad4 SAS
AF:
0.138
Gnomad4 FIN
AF:
0.195
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.254
Alfa
AF:
0.292
Hom.:
3701
Bravo
AF:
0.266
Asia WGS
AF:
0.0830
AC:
293
AN:
3478

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 submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.4
DANN
Benign
0.36

Splicing

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.

Other links and lift over

dbSNP: rs7238897; hg19: chr18-55213058; API