13-113129470-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000375559.8(F10):c.89A>G(p.Gln30Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q30H) has been classified as Benign.
Frequency
Consequence
ENST00000375559.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F10 | NM_000504.4 | c.89A>G | p.Gln30Arg | missense_variant | 2/8 | ENST00000375559.8 | NP_000495.1 | |
F10-AS1 | NR_126424.1 | n.41+536T>C | intron_variant, non_coding_transcript_variant | |||||
F10 | NM_001312674.2 | c.89A>G | p.Gln30Arg | missense_variant | 2/7 | NP_001299603.1 | ||
F10 | NM_001312675.2 | c.89A>G | p.Gln30Arg | missense_variant | 2/8 | NP_001299604.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F10 | ENST00000375559.8 | c.89A>G | p.Gln30Arg | missense_variant | 2/8 | 1 | NM_000504.4 | ENSP00000364709 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Factor X deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Apr 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.