19-6380286-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002096.3(GTF2F1):c.1549G>A(p.Glu517Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002096.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1549G>A | p.Glu517Lys | missense_variant | Exon 13 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.1297G>A | p.Glu433Lys | missense_variant | Exon 10 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.906G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.*105G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1549G>A (p.E517K) alteration is located in exon 13 (coding exon 13) of the GTF2F1 gene. This alteration results from a G to A substitution at nucleotide position 1549, causing the glutamic acid (E) at amino acid position 517 to be replaced by a lysine (K). 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
Publications
No publications associated with this variant yet.