X-154930621-C-T

Position:

chrX-154930621-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 1P and 3B. PP5BP4BS1_SupportingBS2_Supporting

The NM_000132.4(F8):c.3169G>A(p.Glu1057Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 in 1,207,994 control chromosomes in the GnomAD database, including 8 homozygotes. There are 166 hemizygotes in GnomAD. 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 0.00025 ( 0 hom., 6 hem., cov: 23)

Exomes 𝑓: 0.00041 ( 8 hom. 160 hem. )

Consequence

F8
NM_000132.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:5U:3

Conservation

PhyloP100: 0.733

Variant links:

Genes affected

F8 (HGNC:3546): (coagulation factor VIII) This gene encodes coagulation factor VIII, which participates in the intrinsic pathway of blood coagulation; factor VIII is a cofactor for factor IXa which, in the presence of Ca+2 and phospholipids, converts factor X to the activated form Xa. This gene produces two alternatively spliced transcripts. Transcript variant 1 encodes a large glycoprotein, isoform a, which circulates in plasma and associates with von Willebrand factor in a noncovalent complex. This protein undergoes multiple cleavage events. Transcript variant 2 encodes a putative small protein, isoform b, which consists primarily of the phospholipid binding domain of factor VIIIc. This binding domain is essential for coagulant activity. Defects in this gene results in hemophilia A, a common recessive X-linked coagulation disorder. [provided by RefSeq, Jul 2008]

F8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PP5

Variant X-154930621-C-T is Pathogenic according to our data. Variant chrX-154930621-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 10251.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Likely_pathogenic=3, Uncertain_significance=4}. Variant chrX-154930621-C-T is described in Lovd as [Likely_pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.16821963). . Strength limited to SUPPORTING due to the PP5.

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000412 (452/1095913) while in subpopulation EAS AF= 0.0138 (416/30187). AF 95% confidence interval is 0.0127. There are 8 homozygotes in gnomad4_exome. There are 160 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Hemizygotes in GnomAd4 at 6 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F8	NM_000132.4 linkuse as main transcript	c.3169G>A	p.Glu1057Lys	missense_variant	14/26	ENST00000360256.9	NP_000123.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F8	ENST00000360256.9 linkuse as main transcript	c.3169G>A	p.Glu1057Lys	missense_variant	14/26	1	NM_000132.4	ENSP00000353393	P1	P00451-1
F8	ENST00000647125.1 linkuse as main transcript	c.*2835G>A		3_prime_UTR_variant, NMD_transcript_variant	14/14			ENSP00000496062

Frequencies

GnomAD3 genomes

AF:

0.000241

AC:

AN:

112031

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

34231

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00667

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000564

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000591

AC:

108

AN:

182664

Hom.:

AF XY:

0.000534

AC XY:

AN XY:

67362

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00707

Gnomad SAS exome

AF:

0.000158

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000614

Gnomad OTH exome

AF:

0.000445

GnomAD4 exome

AF:

0.000412

AC:

452

AN:

1095913

Hom.:

Cov.:

AF XY:

0.000443

AC XY:

160

AN XY:

361351

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0138

Gnomad4 SAS exome

AF:

0.000148

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000131

Gnomad4 OTH exome

AF:

0.000326

GnomAD4 genome

AF:

0.000250

AC:

AN:

112081

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

34291

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00669

Gnomad4 SAS

AF:

0.000370

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000565

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000334

Hom.:

Bravo

AF:

0.000230

ExAC

AF:

0.000634

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:5Uncertain:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hereditary factor VIII deficiency disease

Pathogenic:4Uncertain:2

Likely pathogenic, criteria provided, single submitter	reference population	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	Mar 18, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	UCLA Clinical Genomics Center, UCLA	Apr 16, 2013	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 01, 1993	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The p.Glu1057Lys (NM_000132.3 c.3169G>A) variant in F8 has been reported hemizygously in three males with Hemophilia A and low factor VIII levels, though one of these individuals carried a second pathogenic variant (Higuchi 1991, Chan 1996, Huang 2009). This variant has also been reported in ClinVar (Variation ID#10251). This variant has been identified in 0.7% (95/13902) of East Asian chromosomes, including 1 homozygote and 29 hemizygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs28933673). In vitro functional studies provide some evidence that the p.Glu1057Lys variant may impact protein function (Pahl 2014); however, these types of assays may not accurately represent biological function. In summary, while there is some suspicion for a pathogenic role, the clinical significance of the p.Glu1057Lys variant is uncertain. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Immunology and Genetics Kaiserslautern	Aug 05, 2022	ACMG Criteria: PS3, PP2, PP3, PP5; Variant was found in heterozygous state. -
Uncertain significance, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with haemophilia A (MIM#306700). (I) 0109 - This gene is associated with X-linked recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine. (I) 0253 - This variant is hemizygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (71 heterozygotes, 1 homozygote, 36 hemizygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated B domain (PMID: 24108539). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. It has been reported in at least three individuals with haemophilia A (PMIDs: 1924291, 19719548, 30913330). It has also been reported as polymorphism in a haemophilia A cohort, and as hemizygous in an individual with haemophilia B (PMIDs: 18479430, 29296726). It has been reported as both likely pathogenic and uncertain significance in ClinVar. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1010 - Functional evidence for this variant is inconclusive. Authors of a functional study using transfected HEK cells described that the variant protein had mildly decreased factor VIII activity and significantly reduced thermostability (PMID: 24108539), however their raw data was incomplete and not convincing. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Thrombophilia, X-linked, due to factor 8 defect

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Mendelics

May 04, 2022

- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Nov 03, 2023

Variant summary: F8 c.3169G>A (p.Glu1057Lys) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00059 in 182664 control chromosomes, predominantly at a frequency of 0.0071 within the East Asian subpopulation in the gnomAD database, including 1 homozygote and 36 hemizygotes across the subpopulations. This frequency is not significantly higher than estimated for a pathogenic variant in F8 causing Factor VIII Deficiency (Hemophilia A) (0.00059 vs 0.0098), allowing no conclusion about variant significance. c.3169G>A has been reported in the literature in individuals affected with Factor VIII Deficiency (Hemophilia A) without strong evidence of causality (e.g. Higuchi_1991b, Chan_1996, Hwang_2009, Luu_2019, Li_2020, Chen_2021). These reports do not provide unequivocal conclusions about association of the variant with Factor VIII Deficiency (Hemophilia A). At least one publication reports experimental evidence evaluating an impact on protein function, finding that the variant results in reduced FVIII activity and antigen values in HEK293T cells (Pahl_2014). The following publications have been ascertained in the context of this evaluation (PMID: 1924291, 8639447, 19719548, 29296726, 32190902, 34272389, 33706050, 33245802, 35770352, 30913330, 24108539). Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as uncertain significance (n=2), likely pathogenic (n=1) or pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Uncertain

0.029

BayesDel_noAF

Pathogenic

0.27

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.42

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.63

M_CAP

Pathogenic

0.97

MetaRNN

Benign

0.17

MetaSVM

Uncertain

0.72

MutationAssessor

Benign

1.6

MutationTaster

Benign

9.6e-10

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.99

REVEL

Pathogenic

0.65

Sift

Uncertain

0.010

Sift4G

Uncertain

0.035

Polyphen

0.68

Vest4

0.65

MVP

0.99

MPC

0.15

ClinPred

0.035

GERP RS

2.9

Varity_R

0.16

gMVP

0.72

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over