chr13-113106850-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000375581.3(F7):c.70G>T(p.Val24Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000562 in 1,601,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000375581.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
F7 | NM_019616.4 | c.64+945G>T | intron_variant | ENST00000346342.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F7 | ENST00000375581.3 | c.70G>T | p.Val24Phe | missense_variant | 2/9 | 1 | A2 | ||
F7 | ENST00000346342.8 | c.64+945G>T | intron_variant | 1 | NM_019616.4 | P2 | |||
F7 | ENST00000541084.5 | c.64+945G>T | intron_variant | 2 | |||||
F7 | ENST00000444337.1 | c.64+945G>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000174 AC: 4AN: 229552Hom.: 0 AF XY: 0.0000160 AC XY: 2AN XY: 124702
GnomAD4 exome AF: 0.00000552 AC: 8AN: 1449678Hom.: 0 Cov.: 31 AF XY: 0.00000417 AC XY: 3AN XY: 720100
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151998Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74236
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.70G>T (p.V24F) alteration is located in exon 2 (coding exon 2) of the F7 gene. This alteration results from a G to T substitution at nucleotide position 70, causing the valine (V) at amino acid position 24 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at