2-48646734-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006872.5(GTF2A1L):c.670G>A(p.Glu224Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GTF2A1L | NM_006872.5 | c.670G>A | p.Glu224Lys | missense_variant | 6/9 | ENST00000403751.8 | NP_006863.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GTF2A1L | ENST00000403751.8 | c.670G>A | p.Glu224Lys | missense_variant | 6/9 | 1 | NM_006872.5 | ENSP00000384597.3 | ||
STON1-GTF2A1L | ENST00000394754.5 | c.2782G>A | p.Glu928Lys | missense_variant | 8/11 | 1 | ENSP00000378236.1 | |||
ENSG00000279956 | ENST00000602369.3 | n.*408-120C>T | intron_variant | 5 | ENSP00000473498.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248998Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134786
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727232
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2024 | The c.2782G>A (p.E928K) alteration is located in exon 8 (coding exon 7) of the STON1-GTF2A1L gene. This alteration results from a G to A substitution at nucleotide position 2782, causing the glutamic acid (E) at amino acid position 928 to be replaced by a lysine (K). 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