X-139530773-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000133.4(F9):āc.9C>Gā(p.Arg3=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,208,202 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. R3R) has been classified as Likely benign.
Frequency
Consequence
NM_000133.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F9 | NM_000133.4 | c.9C>G | p.Arg3= | synonymous_variant | 1/8 | ENST00000218099.7 | |
F9 | NM_001313913.2 | c.9C>G | p.Arg3= | synonymous_variant | 1/7 | ||
F9 | XM_005262397.5 | c.9C>G | p.Arg3= | synonymous_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F9 | ENST00000218099.7 | c.9C>G | p.Arg3= | synonymous_variant | 1/8 | 1 | NM_000133.4 | P1 | |
F9 | ENST00000394090.2 | c.9C>G | p.Arg3= | synonymous_variant | 1/7 | 1 | |||
F9 | ENST00000479617.2 | n.16C>G | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112347Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34515
GnomAD4 exome AF: 9.13e-7 AC: 1AN: 1095855Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 361403
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112347Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34515
ClinVar
Submissions by phenotype
Hereditary factor IX deficiency disease;C2749016:Thrombophilia, X-linked, due to factor 9 defect Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at