rs1800292

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BA1BP4

This summary comes from the ClinGen Evidence Repository: The c.3864A>C (p.Ser1288=) variant is reported at an MAF of 0.3377 (6437/19059 alleles) in the South Asian population in gnomAD v2.1.,1 with 3958 hemizygotes and 424 homozygotes, meeting BA1 criteria of MAF > 0.000333. The synonymous variant is predicted to have no impact on splicing based on SpliceAI score of 0.0, meeting BP4. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8/F9: BA1, BP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA343867/MONDO:0010602/071

Frequency

Genomes: 𝑓 0.10 ( 553 hom., 3346 hem., cov: 22)
Exomes 𝑓: 0.11 ( 5194 hom. 41809 hem. )

Consequence

F8
NM_000132.4 synonymous

Scores

2

Clinical Significance

Benign reviewed by expert panel B:9

Conservation

PhyloP100: 0.915
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
For more information check the summary or visit ClinGen Evidence Repository.
BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
F8NM_000132.4 linkc.3864A>C p.Ser1288Ser synonymous_variant Exon 14 of 26 ENST00000360256.9 NP_000123.1 P00451-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
F8ENST00000360256.9 linkc.3864A>C p.Ser1288Ser synonymous_variant Exon 14 of 26 1 NM_000132.4 ENSP00000353393.4 P00451-1
F8ENST00000647125.1 linkn.*3530A>C downstream_gene_variant ENSP00000496062.1 A0A2R8Y7J7

Frequencies

GnomAD3 genomes
AF:
0.100
AC:
11138
AN:
111284
Hom.:
555
Cov.:
22
AF XY:
0.0998
AC XY:
3343
AN XY:
33510
show subpopulations
Gnomad AFR
AF:
0.0677
Gnomad AMI
AF:
0.118
Gnomad AMR
AF:
0.193
Gnomad ASJ
AF:
0.181
Gnomad EAS
AF:
0.163
Gnomad SAS
AF:
0.350
Gnomad FIN
AF:
0.0506
Gnomad MID
AF:
0.159
Gnomad NFE
AF:
0.0844
Gnomad OTH
AF:
0.131
GnomAD3 exomes
AF:
0.147
AC:
26861
AN:
182684
Hom.:
1653
AF XY:
0.155
AC XY:
10429
AN XY:
67466
show subpopulations
Gnomad AFR exome
AF:
0.0669
Gnomad AMR exome
AF:
0.262
Gnomad ASJ exome
AF:
0.174
Gnomad EAS exome
AF:
0.165
Gnomad SAS exome
AF:
0.338
Gnomad FIN exome
AF:
0.0578
Gnomad NFE exome
AF:
0.0886
Gnomad OTH exome
AF:
0.146
GnomAD4 exome
AF:
0.106
AC:
116489
AN:
1097891
Hom.:
5194
Cov.:
33
AF XY:
0.115
AC XY:
41809
AN XY:
363287
show subpopulations
Gnomad4 AFR exome
AF:
0.0645
Gnomad4 AMR exome
AF:
0.252
Gnomad4 ASJ exome
AF:
0.175
Gnomad4 EAS exome
AF:
0.117
Gnomad4 SAS exome
AF:
0.340
Gnomad4 FIN exome
AF:
0.0612
Gnomad4 NFE exome
AF:
0.0845
Gnomad4 OTH exome
AF:
0.130
GnomAD4 genome
AF:
0.0999
AC:
11128
AN:
111341
Hom.:
553
Cov.:
22
AF XY:
0.0997
AC XY:
3346
AN XY:
33577
show subpopulations
Gnomad4 AFR
AF:
0.0676
Gnomad4 AMR
AF:
0.193
Gnomad4 ASJ
AF:
0.181
Gnomad4 EAS
AF:
0.163
Gnomad4 SAS
AF:
0.347
Gnomad4 FIN
AF:
0.0506
Gnomad4 NFE
AF:
0.0845
Gnomad4 OTH
AF:
0.130
Alfa
AF:
0.0975
Hom.:
2697
Bravo
AF:
0.108
EpiCase
AF:
0.0980
EpiControl
AF:
0.0931

ClinVar

Significance: Benign
Submissions summary: Benign:9
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not specified Benign:3
-
Genome Diagnostics Laboratory, University Medical Center Utrecht
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

-
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:3
Nov 11, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Nov 11, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Hereditary factor VIII deficiency disease Benign:3
Aug 10, 2021
Genome-Nilou Lab
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 01, 2024
ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen
Significance: Benign
Review Status: reviewed by expert panel
Collection Method: curation

The c.3864A>C (p.Ser1288=) variant is reported at an MAF of 0.3377 (6437/19059 alleles) in the South Asian population in gnomAD v2.1.,1 with 3958 hemizygotes and 424 homozygotes, meeting BA1 criteria of MAF > 0.000333. The synonymous variant is predicted to have no impact on splicing based on SpliceAI score of 0.0, meeting BP4. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F8/F9: BA1, BP4. -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.1
DANN
Benign
0.59

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.

Other links and lift over

dbSNP: rs1800292; hg19: chrX-154158201; COSMIC: COSV64272682; COSMIC: COSV64272682; API