1-241500602-TGAGAGAGAGAGAGAGAGA-TGAGAGAGAGAGAGAGAGAGAGAGA

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_000143.4(FH):​c.1237-18_1237-13dupTCTCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.20 ( 2680 hom., cov: 0)
Exomes 𝑓: 0.15 ( 564 hom. )
Failed GnomAD Quality Control

Consequence

FH
NM_000143.4 intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4B:3

Conservation

PhyloP100: -0.993
Variant links:
Genes affected
FH (HGNC:3700): (fumarate hydratase) The protein encoded by this gene is an enzymatic component of the tricarboxylic acid (TCA) cycle, or Krebs cycle, and catalyzes the formation of L-malate from fumarate. It exists in both a cytosolic form and an N-terminal extended form, differing only in the translation start site used. The N-terminal extended form is targeted to the mitochondrion, where the removal of the extension generates the same form as in the cytoplasm. It is similar to some thermostable class II fumarases and functions as a homotetramer. Mutations in this gene can cause fumarase deficiency and lead to progressive encephalopathy. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 1-241500602-T-TGAGAGA is Benign according to our data. Variant chr1-241500602-T-TGAGAGA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 296867.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=4, Benign=1, Likely_benign=2}.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FHNM_000143.4 linkc.1237-18_1237-13dupTCTCTC intron_variant Intron 8 of 9 ENST00000366560.4 NP_000134.2 P07954-1A0A0S2Z4C3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FHENST00000366560.4 linkc.1237-18_1237-13dupTCTCTC intron_variant Intron 8 of 9 1 NM_000143.4 ENSP00000355518.4 P07954-1

Frequencies

GnomAD3 genomes
AF:
0.202
AC:
26994
AN:
133502
Hom.:
2678
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.150
Gnomad AMR
AF:
0.188
Gnomad ASJ
AF:
0.192
Gnomad EAS
AF:
0.172
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.174
Gnomad MID
AF:
0.184
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.199
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.152
AC:
202299
AN:
1326574
Hom.:
564
Cov.:
48
AF XY:
0.151
AC XY:
99564
AN XY:
659940
show subpopulations
Gnomad4 AFR exome
AF:
0.142
Gnomad4 AMR exome
AF:
0.104
Gnomad4 ASJ exome
AF:
0.126
Gnomad4 EAS exome
AF:
0.119
Gnomad4 SAS exome
AF:
0.133
Gnomad4 FIN exome
AF:
0.115
Gnomad4 NFE exome
AF:
0.160
Gnomad4 OTH exome
AF:
0.148
GnomAD4 genome
AF:
0.202
AC:
27016
AN:
133592
Hom.:
2680
Cov.:
0
AF XY:
0.201
AC XY:
12811
AN XY:
63710
show subpopulations
Gnomad4 AFR
AF:
0.175
Gnomad4 AMR
AF:
0.188
Gnomad4 ASJ
AF:
0.192
Gnomad4 EAS
AF:
0.172
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.174
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.200

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:4Benign:3
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Hereditary leiomyomatosis and renal cell cancer Uncertain:2
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not specified Uncertain:1Benign:1
Jul 12, 2017
Genetic Services Laboratory, University of Chicago
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:2
Aug 30, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Aug 12, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Fumarase deficiency Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs144131869; hg19: chr1-241663902; API