19-6380339-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_002096.3(GTF2F1):c.1496G>A(p.Arg499Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1496G>A | p.Arg499Gln | missense_variant | Exon 13 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.1244G>A | p.Arg415Gln | missense_variant | Exon 10 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.853G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.*52G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251496Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135922
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1496G>A (p.R499Q) 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 1496, causing the arginine (R) at amino acid position 499 to be replaced by a glutamine (Q). 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