chr2-48646978-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006872.5(GTF2A1L):c.914G>A(p.Gly305Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,978 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 Uncertain significance (★).
Frequency
Consequence
NM_006872.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF2A1L | NM_006872.5 | c.914G>A | p.Gly305Glu | missense_variant | 6/9 | ENST00000403751.8 | |
STON1-GTF2A1L | NM_001198593.2 | c.3026G>A | p.Gly1009Glu | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2A1L | ENST00000403751.8 | c.914G>A | p.Gly305Glu | missense_variant | 6/9 | 1 | NM_006872.5 | P1 | |
GTF2A1L | ENST00000430487.6 | c.812G>A | p.Gly271Glu | missense_variant | 5/8 | 2 | |||
GTF2A1L | ENST00000437125.5 | c.941G>A | p.Gly314Glu | missense_variant | 6/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248346Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134524
GnomAD4 exome AF: 0.0000752 AC: 110AN: 1461810Hom.: 0 Cov.: 33 AF XY: 0.0000866 AC XY: 63AN XY: 727200
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 05, 2023 | The c.914G>A (p.G305E) alteration is located in exon 6 (coding exon 6) of the GTF2A1L gene. This alteration results from a G to A substitution at nucleotide position 914, causing the glycine (G) at amino acid position 305 to be replaced by a glutamic acid (E). 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