chr13-113129541-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The ENST00000375559.8(F10):c.160G>A(p.Glu54Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E54G) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000375559.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
F10 | NM_000504.4 | c.160G>A | p.Glu54Lys | missense_variant | 2/8 | ENST00000375559.8 | NP_000495.1 | |
F10-AS1 | NR_126424.1 | n.41+465C>T | intron_variant, non_coding_transcript_variant | |||||
F10 | NM_001312674.2 | c.160G>A | p.Glu54Lys | missense_variant | 2/7 | NP_001299603.1 | ||
F10 | NM_001312675.2 | c.160G>A | p.Glu54Lys | missense_variant | 2/8 | NP_001299604.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F10 | ENST00000375559.8 | c.160G>A | p.Glu54Lys | missense_variant | 2/8 | 1 | NM_000504.4 | ENSP00000364709 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461876Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Factor X deficiency Pathogenic:1Uncertain:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 15, 1990 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Hereditary factor X deficiency disease Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | NIHR Bioresource Rare Diseases, University of Cambridge | Feb 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at