3-120781366-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005513.3(GTF2E1):āc.1216A>Gā(p.Ser406Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,613,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005513.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2E1 | NM_005513.3 | c.1216A>G | p.Ser406Gly | missense_variant | 5/5 | ENST00000283875.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2E1 | ENST00000283875.6 | c.1216A>G | p.Ser406Gly | missense_variant | 5/5 | 1 | NM_005513.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251046Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135654
GnomAD4 exome AF: 0.000115 AC: 168AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.000116 AC XY: 84AN XY: 727194
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2023 | The c.1216A>G (p.S406G) alteration is located in exon 5 (coding exon 4) of the GTF2E1 gene. This alteration results from a A to G substitution at nucleotide position 1216, causing the serine (S) at amino acid position 406 to be replaced by a glycine (G). 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