rs1800730

chr6-26090957-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM1 BP4_Strong BS1 BS2

The NM_000410.4(HFE):c.193A>T(p.Ser65Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0136 in 1,614,088 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.010 (12 hom., cov: 31)
  • Exomes 𝑓: 0.014 (183 hom.)
• Consequence: HFE NM_000410.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:10 B:3 O:1
• Conservation: PhyloP100: 5.10

Genes affected

HFE (HGNC:4886): (homeostatic iron regulator) The protein encoded by this gene is a membrane protein that is similar to MHC class I-type proteins and associates with beta2-microglobulin (beta2M). It is thought that this protein functions to regulate iron absorption by regulating the interaction of the transferrin receptor with transferrin. The iron storage disorder, hereditary haemochromatosis, is a recessive genetic disorder that results from defects in this gene. [provided by RefSeq, May 2022]

HFE-AS1 (HGNC:):

H2BC4 (HGNC:4757): (H2B clustered histone 4) Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. The protein has antibacterial and antifungal antimicrobial activity. The main transcript variant of this gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. This transcript variant lacks a polyA tail but instead contains a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Apr 2020]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• PM1: In a region_of_interest Alpha-1 (size 91) in uniprot entity HFE_HUMAN there are 7 pathogenic changes around while only 3 benign (70%) in NM_000410.4
• BP4: Computational evidence support a benign effect (MetaRNN=0.01902759).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00995 (1515/152208) while in subpopulation NFE AF= 0.0154 (1044/68008). AF 95% confidence interval is 0.0146. There are 12 homozygotes in gnomad4. There are 756 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 12 AR,Digenic gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HFE	NM_000410.4	c.193A>T	p.Ser65Cys	missense_variant	2/6	ENST00000357618.10
HFE-AS1	NR_144383.1	n.78T>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HFE	ENST00000357618.10	c.193A>T	p.Ser65Cys	missense_variant	2/6	1	NM_000410.4	P3

Frequencies

GnomAD3 genomes AF: 0.00997 AC: 1516 AN: 152090 Hom.: 12 Cov.: 31

Gnomad AFR AF: 0.00290

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.00668

Gnomad ASJ AF: 0.00260

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.00526

GnomAD3 exomes AF: 0.0102 AC: 2575 AN: 251490 Hom.: 24 AF XY: 0.0101 AC XY: 1369 AN XY: 135920

Gnomad AFR exome AF: 0.00234

Gnomad AMR exome AF: 0.00489

Gnomad ASJ exome AF: 0.00347

Gnomad EAS exome AF: 0.000217

Gnomad SAS exome AF: 0.000980

Gnomad FIN exome AF: 0.0217

Gnomad NFE exome AF: 0.0155

Gnomad OTH exome AF: 0.0103

GnomAD4 exome AF: 0.0140 AC: 20501 AN: 1461880 Hom.: 183 Cov.: 34 AF XY: 0.0137 AC XY: 9989 AN XY: 727244

Gnomad4 AFR exome AF: 0.00209

Gnomad4 AMR exome AF: 0.00474

Gnomad4 ASJ exome AF: 0.00306

Gnomad4 EAS exome AF: 0.000151

Gnomad4 SAS exome AF: 0.000997

Gnomad4 FIN exome AF: 0.0228

Gnomad4 NFE exome AF: 0.0163

Gnomad4 OTH exome AF: 0.0111

GnomAD4 genome AF: 0.00995 AC: 1515 AN: 152208 Hom.: 12 Cov.: 31 AF XY: 0.0102 AC XY: 756 AN XY: 74416

Gnomad4 AFR AF: 0.00289

Gnomad4 AMR AF: 0.00667

Gnomad4 ASJ AF: 0.00260

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.000830

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0154

Gnomad4 OTH AF: 0.00520

Alfa AF: 0.0136 Hom.: 11

Bravo AF: 0.00887

TwinsUK AF: 0.0135 AC: 50

ALSPAC AF: 0.0138 AC: 53

ESP6500AA AF: 0.00318 AC: 14

ESP6500EA AF: 0.0151 AC: 130

ExAC AF: 0.0101 AC: 1225

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:10 Benign:3 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hemochromatosis type 1 Pathogenic:2 Uncertain:2 Other:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 15, 1999	- -
Pathogenic, no assertion criteria provided	clinical testing	Blueprint Genetics	Nov 11, 2014	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jul 27, 2017	The HFE c.193A>T (p.Ser65Cys) variant is a missense variant that has been reported to be enriched in individuals affected with hereditary hemochromatosis as compared to unaffected individuals in two studies (Mura et al. 1999; Holmstrom et al. 2002). The authors suggested that the p.Ser65Cys variant is associated with a mild phenotype, resulting in a lower degree of iron overload as compared to common pathogenic variants in the HFE gene. Two functional studies have reported that the p.Ser65Cys variant alone has no significant influence on iron status markers (Pedersen et al. 2009; Aranda et al. 2010), and Bacon et al. (2011) and Alves et al. (2016) discuss that the p.Ser65Cys variant is generally not associated with iron loading unless seen in a compound heterozygous state with either the p.Cys282Tyr or p.His63Asp variant. The p.Ser65Cys variant is reported at a frequency of 0.03846 in the British of England and Scotland population of the 1000 Genomes Project, which is consistent with estimates of disease prevalence and penetrance. Although p.Ser65Cys variant is widely reported in the literature as the third most common variant associated with HFE-related hereditary hemochromatosis (Seckington et al. 2015), the functional evidence suggests that this variant may not contribute to the mechanism of disease. Based on this conflicting evidence, the p.Ser65Cys is classified as a variant of unknown significance but suspicious for pathogenicity for hereditary hemochromatosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Dec 07, 2021	_x000D_This variant was identified as compound heterozygous with NM_000410.4:c.845G>A. Criteria applied: PM3, PP3, BS3_SUP -

not provided Uncertain:2 Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 19, 2018	This variant is associated with the following publications: (PMID: 10792295, 31664448, 31016714, 31028937, 29431110, 12377814, 28280078, 10194428, 19159930, 16132052, 10660483, 20301613, 27221532, 27173269, 26153218, 20107990, 21452290, 18542962, 17124037, 11336458, 27153395, 20981092, 19271219, 19681031) -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 30, 2022	The p.Ser65Cys has been reported as a normal variant in the European population, has also been described as a susceptibility allele in patients with iron overload, particularly in association with heavy alcohol consumption,but no evidence has ever been provided to support a causative role in HH. Therefore, neither testing nor reporting the presence of p.Ser65Cys is recommended in the diagnosis of HFE-related HH (EMQN best practice guidelines for the molecular genetic diagnosis of hereditary hemochromatosis (HH) PMID: 26153218). Also: A third HFE genotype, known as type 1c, is related to the mutation Ser65Cys. The Ser65Cys mutation may lead to increased serum iron and ferritin levels but has not been associated with excess tissue iron stores and can, therefore, be considered a polymorphism without clinical significance (ACG Clinical Guideline: Hereditary Hemochromatosis). The Ser65Cys mutation is less common than either C282Y or H63D, with a heterozygote frequency of about 2% among whites (113,114). This mutation appears to have a modest effect on iron metabolism in the presence of the C282Y mutation, but iron overload–related disease has not been reported in C282Y/S65C compound heterozygotes. Neither the homozygous nor the heterozygous H63D or S65C mutation is a cause of pathologic iron overload. (PMID: 31335359). Furthermore, in this batch, the variant is detected in the heterozygous state in an individual who does not carry the C282Y variant. -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Apr 01, 2024	HFE: BS1, BS2 -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The HFE c.193A>T (p.Ser65Cys) variant was identified in the literature in multiple studies investigating the relationship between HFE variants and hemochromatosis or iron overload. A study of 711 patients with hemochromatosis found that the S65C variant was enriched in individuals with hemochromatosis in the absence of the two classical hemochromatosis variants (C282Y and H63D), with an affected frequency of 0.078 and a control frequency of 0.025. This study suggested that the S65C variant is associated with a mild form of hemochromatosis (Mura_1999_PMID:10194428). The p.S65C variant was also found in 14/296 patients with iron overload (freq=0.024) and 8/250 healthy controls (freq=0.016), suggesting that the variant may contribute to mild iron overload (Holmstrom_2002_PMID: 12377814). However, more recent studies have disputed the role of the S65C variant in hemochromatosis and iron status. A study of HFE polymorphisms in a Spanish Mediterranean population and another study of 6,020 Danish men both found no effect of the S65C variant on iron status (Aranda_2010_PMID: 20107990; Pedersen_2009_PMID:19159930). This variant was also identified in dbSNP (ID: rs1800730), ClinVar (classified as a VUS by Invitae and Illumina and as pathogenic by Blueprint Genetics for hereditary hemochromatosis) and LOVD 3.0, but was not reported in Cosmic. The variant was identified in control databases in 2891 of 282878 chromosomes (24 homozygous) at a frequency of 0.01022 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (Finnish) in 537 of 25120 chromosomes (freq: 0.02138), European (non-Finnish) in 1977 of 129196 chromosomes (freq: 0.0153), Other in 72 of 7226 chromosomes (freq: 0.009964), Latino in 173 of 35440 chromosomes (freq: 0.004881), Ashkenazi Jewish in 35 of 10370 chromosomes (freq: 0.003375), African in 63 of 24958 chromosomes (freq: 0.002524), South Asian in 30 of 30616 chromosomes (freq: 0.00098), and East Asian in 4 of 19952 chromosomes (freq: 0.000201). The p.Ser65 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance, however we would suggest that this variant may be a risk factor for hemochromatosis. -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 26, 2021	Variant summary: HFE c.193A>T (p.Ser65Cys) results in a non-conservative amino acid change located in the MHC class I-like antigen recognition-like domain (IPR011161) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.01 in 251490 control chromosomes in the gnomAD database, including 24 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in HFE causing Hemochromatosis Type 1 (0.01 vs 0.046), allowing no conclusion about variant significance. c.193A>T has been reported in association with Hemochromatosis Type 1 in at least one published study, in which the variant was enriched in individuals affected with Hemochromatosis who did not have two alleles with some combination of the more common disease mutations p.C282Y and p.H63D (e.g. Mura_1999). This data suggested a possibly pathogenic role for the p.S65C variant. However, the variant has also been found in compound heterozygosity with these other disease variants in controls, and additional studies did not find association of the variant with the Hemochromatosis phenotype (e.g. Arya_1999, Oliveira_2009, Pedersen_2009). At least one publication reported an association for the variant with mild to moderate changes in serum ferritin and/or transferrin levels in indivduals who were compound heterozygotes for this variant and one of the common disease variants, however these individuals did not have clinical symptoms of iron load typically found in patients diagnosed with Hemochromatosis Type 1 (e.g. Holmstrom_2002). These reports do not provide unequivocal conclusions about association of the variant with Hemochromatosis Type 1. To our knowledge, no conclusive experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) have cited the variant as uncertain significance (n=4) and likely pathogenic (n=1). Based on the majority concordance in its classification among peers in the field supported by the evidence outlined above, the variant was classified as uncertain significance until additional information becomes available. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -

HFE-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 20, 2024

The HFE c.193A>T variant is predicted to result in the amino acid substitution p.Ser65Cys. Reports have indicated that the c.193A>T variant may be involved in a mild form of hemochromatosis (Mura et al. 1999. PubMed ID: 10194428; Holmström et al. 2002. PubMed ID: 12377814). However, a different study found no significant changes in ferritin levels in individuals with the p.Ser65Cys variant, even in presence of a corresponding p.Cys282Tyr or p.His63Asp variant (Pedersen and Milman. 2009. PubMed ID: 19159930). This variant has conflicting interpretations ranging from benign to uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/11/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Alzheimer disease;C0162532:Variegate porphyria;C0268323:Familial porphyria cutanea tarda;C2673520:Microvascular complications of diabetes, susceptibility to, 7;C3280096:Transferrin serum level quantitative trait locus 2;C3469186:Hemochromatosis type 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Variegate porphyria;C0268323:Familial porphyria cutanea tarda;C1863052:Alzheimer disease type 1;C2673520:Microvascular complications of diabetes, susceptibility to, 7;C3280096:Transferrin serum level quantitative trait locus 2;C3469186:Hemochromatosis type 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Mar 30, 2021

HFE NM_000410.3 exon 2 p.Ser65Cys (c.193A>T): This variant has been reported in the literature in the heterozygous or compound heterozygous state in several individuals with hemochromatosis and is reported to be enriched in this population compared to controls (Mura 1999 PMID:10194428, Holstrom 2002 PMID:12377814). However, additional studies did not find this association (Arya 1999 PMID:10660483, Pendersen 2009 PMID:19159930). Some authors suggest that this variant may act as a risk allele or low penetrance variant when in trans with the Cys282Tyr or His63Asp variants (Wallace 2002 PMID:11943417, Le Gac 2005 PMID:16132052). This variant is also present in 1% (2891/282878) of total alleles in the Genome Aggregation Database, including 24 homozygotes (https://gnomad.broadinstitute.org/variant/6-26091185-A-T). This variant is present in ClinVar (Variation ID:11). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -

Hereditary hemochromatosis Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Benign	-0.094	T
BayesDel_noAF	Uncertain	0.11
Cadd	Uncertain	25
Dann	Uncertain	0.99
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Benign	0.72	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D;D
MetaRNN	Benign	0.019	T;T;T;T;T;T;T
MetaSVM	Uncertain	0.65	D
MutationTaster	Benign	0.69	A;A;A;A;A;A;A;A;A;A;A
PrimateAI	Benign	0.44	T
PROVEAN	Uncertain	-2.6	D;D;D;D;D;D;D
REVEL	Uncertain	0.55
Sift	Uncertain	0.0010	D;D;D;D;D;D;D
Sift4G	Uncertain	0.0030	D;D;D;D;D;D;D
Polyphen		0.99	D;D;D;D;D;D;.
Vest4		0.32
MPC		0.82
ClinPred		0.071	T
GERP RS		4.1
Varity_R		0.79
gMVP		0.92

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: rs1800730; hg19: chr6-26091185;