1-241500602-TGAGAGAGAGAGAGAGAGA-TGAGAGAGAGAGAGAGAGAGAGAGAGAGA

Variant summary

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

The NM_000143.4(FH):​c.1237-22_1237-13dupTCTCTCTCTC 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 0.040 ( 148 hom., cov: 0)
Exomes 𝑓: 0.029 ( 165 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:3B: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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6
Variant 1-241500602-T-TGAGAGAGAGA is Benign according to our data. Variant chr1-241500602-T-TGAGAGAGAGA is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 296869.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=3, Benign=2, Likely_benign=1}.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FHNM_000143.4 linkc.1237-22_1237-13dupTCTCTCTCTC 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.1237-22_1237-13dupTCTCTCTCTC intron_variant Intron 8 of 9 1 NM_000143.4 ENSP00000355518.4 P07954-1

Frequencies

GnomAD3 genomes
AF:
0.0401
AC:
5350
AN:
133524
Hom.:
146
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0573
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0296
Gnomad ASJ
AF:
0.0180
Gnomad EAS
AF:
0.0350
Gnomad SAS
AF:
0.0623
Gnomad FIN
AF:
0.0339
Gnomad MID
AF:
0.0455
Gnomad NFE
AF:
0.0342
Gnomad OTH
AF:
0.0372
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0286
AC:
38329
AN:
1341810
Hom.:
165
Cov.:
48
AF XY:
0.0286
AC XY:
19076
AN XY:
667912
show subpopulations
Gnomad4 AFR exome
AF:
0.0419
Gnomad4 AMR exome
AF:
0.0147
Gnomad4 ASJ exome
AF:
0.0141
Gnomad4 EAS exome
AF:
0.0177
Gnomad4 SAS exome
AF:
0.0380
Gnomad4 FIN exome
AF:
0.0212
Gnomad4 NFE exome
AF:
0.0290
Gnomad4 OTH exome
AF:
0.0294
GnomAD4 genome
AF:
0.0401
AC:
5356
AN:
133612
Hom.:
148
Cov.:
0
AF XY:
0.0405
AC XY:
2584
AN XY:
63738
show subpopulations
Gnomad4 AFR
AF:
0.0574
Gnomad4 AMR
AF:
0.0294
Gnomad4 ASJ
AF:
0.0180
Gnomad4 EAS
AF:
0.0348
Gnomad4 SAS
AF:
0.0625
Gnomad4 FIN
AF:
0.0339
Gnomad4 NFE
AF:
0.0342
Gnomad4 OTH
AF:
0.0373

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign: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 provided Benign:2
Aug 15, 2019
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 29, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
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

- -

not specified Benign:1
Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance: Likely benign
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