rs118203906
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM5PP3_ModeratePP5BS1_Supporting
The NM_000130.5(F5):c.1001G>C(p.Arg334Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,614,068 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic 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. R334G) has been classified as Likely benign.
Frequency
Consequence
NM_000130.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F5 | NM_000130.5 | c.1001G>C | p.Arg334Thr | missense_variant | 7/25 | ENST00000367797.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F5 | ENST00000367797.9 | c.1001G>C | p.Arg334Thr | missense_variant | 7/25 | 1 | NM_000130.5 | P2 | |
F5 | ENST00000367796.3 | c.1001G>C | p.Arg334Thr | missense_variant | 7/25 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000227 AC: 57AN: 251352Hom.: 1 AF XY: 0.000213 AC XY: 29AN XY: 135844
GnomAD4 exome AF: 0.000130 AC: 190AN: 1461852Hom.: 2 Cov.: 31 AF XY: 0.000133 AC XY: 97AN XY: 727226
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74428
ClinVar
Submissions by phenotype
Thrombophilia due to activated protein C resistance Pathogenic:1Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 15, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at