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
Consequence
NM_000132.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F8 | ENST00000360256.9 | c.3864A>C | p.Ser1288Ser | synonymous_variant | Exon 14 of 26 | 1 | NM_000132.4 | ENSP00000353393.4 | ||
F8 | ENST00000647125.1 | n.*3530A>C | downstream_gene_variant | ENSP00000496062.1 |
Frequencies
GnomAD3 genomes AF: 0.100 AC: 11138AN: 111284Hom.: 555 Cov.: 22 AF XY: 0.0998 AC XY: 3343AN XY: 33510
GnomAD3 exomes AF: 0.147 AC: 26861AN: 182684Hom.: 1653 AF XY: 0.155 AC XY: 10429AN XY: 67466
GnomAD4 exome AF: 0.106 AC: 116489AN: 1097891Hom.: 5194 Cov.: 33 AF XY: 0.115 AC XY: 41809AN XY: 363287
GnomAD4 genome AF: 0.0999 AC: 11128AN: 111341Hom.: 553 Cov.: 22 AF XY: 0.0997 AC XY: 3346AN XY: 33577
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:3
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Hereditary factor VIII deficiency disease Benign:3
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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. -
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at