chr13-113105879-T-A
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_019616.4(F7):c.38T>A(p.Leu13His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 1,439,506 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
F7
NM_019616.4 missense
NM_019616.4 missense
Scores
1
10
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.991
Genes affected
F7 (HGNC:3544): (coagulation factor VII) This gene encodes coagulation factor VII which is a vitamin K-dependent factor essential for hemostasis. This factor circulates in the blood in a zymogen form, and is converted to an active form by either factor IXa, factor Xa, factor XIIa, or thrombin by minor proteolysis. Upon activation of the factor VII, a heavy chain containing a catalytic domain and a light chain containing 2 EGF-like domains are generated, and two chains are held together by a disulfide bond. In the presence of factor III and calcium ions, the activated factor then further activates the coagulation cascade by converting factor IX to factor IXa and/or factor X to factor Xa. Defects in this gene can cause coagulopathy. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing to generate mature polypeptides. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
F7 | ENST00000346342.8 | c.38T>A | p.Leu13His | missense_variant | Exon 1 of 8 | 1 | NM_019616.4 | ENSP00000329546.4 | ||
F7 | ENST00000375581.3 | c.38T>A | p.Leu13His | missense_variant | Exon 1 of 9 | 1 | ENSP00000364731.3 | |||
F7 | ENST00000541084.5 | c.38T>A | p.Leu13His | missense_variant | Exon 1 of 6 | 2 | ENSP00000442051.2 | |||
F7 | ENST00000444337.1 | n.38T>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000387669.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.00000462 AC: 1AN: 216450Hom.: 0 AF XY: 0.00000862 AC XY: 1AN XY: 116000
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GnomAD4 exome AF: 0.00000139 AC: 2AN: 1439506Hom.: 0 Cov.: 31 AF XY: 0.00000280 AC XY: 2AN XY: 713336
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GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Uncertain
.;.;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
.;M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N
REVEL
Uncertain
Sift
Uncertain
.;D;D
Sift4G
Pathogenic
D;T;D
Polyphen
1.0, 1.0
.;D;D
Vest4
MutPred
Gain of catalytic residue at G14 (P = 0);Gain of catalytic residue at G14 (P = 0);Gain of catalytic residue at G14 (P = 0);
MVP
MPC
0.24
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at