19-6380930-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002096.3(GTF2F1):c.1205G>A(p.Arg402Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000431 in 1,576,204 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R402W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002096.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1205G>A | p.Arg402Gln | missense_variant | Exon 11 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.953G>A | p.Arg318Gln | missense_variant | Exon 8 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.572G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.523G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152198Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000626 AC: 12AN: 191626Hom.: 0 AF XY: 0.0000575 AC XY: 6AN XY: 104280
GnomAD4 exome AF: 0.0000330 AC: 47AN: 1423888Hom.: 0 Cov.: 33 AF XY: 0.0000298 AC XY: 21AN XY: 705732
GnomAD4 genome AF: 0.000138 AC: 21AN: 152316Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1205G>A (p.R402Q) alteration is located in exon 11 (coding exon 11) of the GTF2F1 gene. This alteration results from a G to A substitution at nucleotide position 1205, causing the arginine (R) at amino acid position 402 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