chr19-6380324-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002096.3(GTF2F1):c.1511G>A(p.Arg504His) variant causes a missense change. The variant allele was found at a frequency of 0.0000954 in 1,614,094 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1511G>A | p.Arg504His | missense_variant | Exon 13 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.1259G>A | p.Arg420His | missense_variant | Exon 10 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.868G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.*67G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251496Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135922
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000866 AC XY: 63AN XY: 727240
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1511G>A (p.R504H) 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 1511, causing the arginine (R) at amino acid position 504 to be replaced by a histidine (H). 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