chr2-48646651-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006872.5(GTF2A1L):āc.587A>Cā(p.Gln196Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 152,216 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 (ā ).
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 | UniProt |
---|---|---|---|---|---|---|---|
GTF2A1L | NM_006872.5 | c.587A>C | p.Gln196Pro | missense_variant | 6/9 | ENST00000403751.8 | |
STON1-GTF2A1L | NM_001198593.2 | c.2699A>C | p.Gln900Pro | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2A1L | ENST00000403751.8 | c.587A>C | p.Gln196Pro | missense_variant | 6/9 | 1 | NM_006872.5 | P1 | |
GTF2A1L | ENST00000430487.6 | c.485A>C | p.Gln162Pro | missense_variant | 5/8 | 2 | |||
GTF2A1L | ENST00000437125.5 | c.614A>C | p.Gln205Pro | missense_variant | 6/6 | 4 | |||
GTF2A1L | ENST00000448460.5 | c.485A>C | p.Gln162Pro | missense_variant | 5/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.587A>C (p.Q196P) alteration is located in exon 6 (coding exon 6) of the GTF2A1L gene. This alteration results from a A to C substitution at nucleotide position 587, causing the glutamine (Q) at amino acid position 196 to be replaced by a proline (P). 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