1-241500602-TGAGAGAGAGAGAGAGAGA-TGAGAGAGAGAGAGAGA

Variant names:

• chr1-241500602-TGA-T
• rs144131869
• NM_000143.4:c.1237-14_1237-13delTC

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_000143.4(FH):​c.1237-14_1237-13delTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 1,479,644 control chromosomes in the GnomAD database, including 99 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.022 (96 hom., cov: 0)
  • Exomes 𝑓: 0.041 (3 hom.)
• Consequence: FH NM_000143.4 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3 B:6
• Conservation: PhyloP100: 2.18

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 1-241500602-TGA-T is Benign according to our data. Variant chr1-241500602-TGA-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 296871.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Uncertain_significance=3}. Variant chr1-241500602-TGA-T is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FH	NM_000143.4	c.1237-14_1237-13delTC		intron_variant	Intron 8 of 9	ENST00000366560.4	NP_000134.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FH	ENST00000366560.4	c.1237-14_1237-13delTC		intron_variant	Intron 8 of 9	1	NM_000143.4	ENSP00000355518.4

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 2928 AN: 133722 Hom.: 96 Cov.: 0

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.00115

Gnomad AMR AF: 0.00935

Gnomad ASJ AF: 0.00244

Gnomad EAS AF: 0.00629

Gnomad SAS AF: 0.00590

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00694

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0124

GnomAD4 exome AF: 0.0408 AC: 54855 AN: 1345834 Hom.: 3 AF XY: 0.0412 AC XY: 27588 AN XY: 669888

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.0807

Gnomad4 ASJ exome AF: 0.0668

Gnomad4 EAS exome AF: 0.112

Gnomad4 SAS exome AF: 0.0425

Gnomad4 FIN exome AF: 0.0526

Gnomad4 NFE exome AF: 0.0329

Gnomad4 OTH exome AF: 0.0476

GnomAD4 genome AF: 0.0220 AC: 2939 AN: 133810 Hom.: 96 Cov.: 0 AF XY: 0.0219 AC XY: 1396 AN XY: 63822

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.00942

Gnomad4 ASJ AF: 0.00244

Gnomad4 EAS AF: 0.00652

Gnomad4 SAS AF: 0.00543

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.00303

Gnomad4 OTH AF: 0.0122

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3 Benign:6

Revision: criteria provided, conflicting classifications

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

-

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Benign:2

Nov 13, 2014

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Mar 16, 2021

Sema4, Sema4

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: curation

- -

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

- -

FH-related disorder Benign:1

Mar 03, 2021

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs144131869; hg19: chr1-241663902;