chr13-113106842-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000375581.3(F7):c.65-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000437 in 1,597,778 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000375581.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F7 | NM_019616.4 | c.64+937C>T | intron_variant | ENST00000346342.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F7 | ENST00000346342.8 | c.64+937C>T | intron_variant | 1 | NM_019616.4 | P2 | |||
F7 | ENST00000375581.3 | c.65-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | A2 | ||||
F7 | ENST00000541084.5 | c.64+937C>T | intron_variant | 2 | |||||
F7 | ENST00000444337.1 | c.64+937C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00233 AC: 354AN: 151968Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000599 AC: 134AN: 223726Hom.: 0 AF XY: 0.000403 AC XY: 49AN XY: 121456
GnomAD4 exome AF: 0.000237 AC: 343AN: 1445692Hom.: 1 Cov.: 31 AF XY: 0.000208 AC XY: 149AN XY: 717742
GnomAD4 genome ? AF: 0.00233 AC: 355AN: 152086Hom.: 2 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74340
ClinVar
Submissions by phenotype
Congenital factor VII deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at