rs387906482
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 7P and 1B. PM1PM2PM5PP5BP4
The NM_000133.4(F9):āc.1031T>Cā(p.Ile344Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000165 in 1,210,422 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. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I344L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000133.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F9 | NM_000133.4 | c.1031T>C | p.Ile344Thr | missense_variant | 8/8 | ENST00000218099.7 | |
F9 | NM_001313913.2 | c.917T>C | p.Ile306Thr | missense_variant | 7/7 | ||
F9 | XM_005262397.5 | c.902T>C | p.Ile301Thr | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F9 | ENST00000218099.7 | c.1031T>C | p.Ile344Thr | missense_variant | 8/8 | 1 | NM_000133.4 | P1 | |
F9 | ENST00000394090.2 | c.917T>C | p.Ile306Thr | missense_variant | 7/7 | 1 | |||
F9 | ENST00000643157.1 | n.1698T>C | non_coding_transcript_exon_variant | 6/7 |
Frequencies
GnomAD3 genomes ? AF: 0.00000891 AC: 1AN: 112243Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34387
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098179Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363543
GnomAD4 genome ? AF: 0.00000891 AC: 1AN: 112243Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34387
ClinVar
Submissions by phenotype
Hereditary factor IX deficiency disease Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at