rs146571246
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002096.3(GTF2F1):c.1511G>T(p.Arg504Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R504H) has been classified 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1511G>T | p.Arg504Leu | missense_variant | Exon 13 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.1259G>T | p.Arg420Leu | missense_variant | Exon 10 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.868G>T | non_coding_transcript_exon_variant | Exon 6 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.*67G>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251496Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135922
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at