chr19-6380961-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002096.3(GTF2F1):c.1174G>A(p.Ala392Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,597,814 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002096.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2F1 | ENST00000394456.10 | c.1174G>A | p.Ala392Thr | missense_variant | Exon 11 of 13 | 1 | NM_002096.3 | ENSP00000377969.3 | ||
GTF2F1 | ENST00000593678.5 | c.922G>A | p.Ala308Thr | missense_variant | Exon 8 of 10 | 2 | ENSP00000469091.1 | |||
GTF2F1 | ENST00000594213.5 | n.541G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 3 | |||||
GTF2F1 | ENST00000594965.1 | n.492G>A | non_coding_transcript_exon_variant | Exon 4 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000135 AC: 3AN: 222482Hom.: 0 AF XY: 0.0000165 AC XY: 2AN XY: 120958
GnomAD4 exome AF: 0.0000159 AC: 23AN: 1445630Hom.: 0 Cov.: 33 AF XY: 0.0000139 AC XY: 10AN XY: 717806
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at