chr2-48646675-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006872.5(GTF2A1L):c.611C>T(p.Pro204Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000429 in 1,614,106 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 (★).
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.611C>T | p.Pro204Leu | missense_variant | 6/9 | ENST00000403751.8 | |
STON1-GTF2A1L | NM_001198593.2 | c.2723C>T | p.Pro908Leu | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF2A1L | ENST00000403751.8 | c.611C>T | p.Pro204Leu | missense_variant | 6/9 | 1 | NM_006872.5 | P1 | |
GTF2A1L | ENST00000430487.6 | c.509C>T | p.Pro170Leu | missense_variant | 5/8 | 2 | |||
GTF2A1L | ENST00000437125.5 | c.638C>T | p.Pro213Leu | missense_variant | 6/6 | 4 | |||
GTF2A1L | ENST00000448460.5 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000478 AC: 119AN: 248878Hom.: 0 AF XY: 0.000445 AC XY: 60AN XY: 134710
GnomAD4 exome AF: 0.000438 AC: 640AN: 1461856Hom.: 0 Cov.: 33 AF XY: 0.000451 AC XY: 328AN XY: 727224
GnomAD4 genome AF: 0.000342 AC: 52AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.611C>T (p.P204L) alteration is located in exon 6 (coding exon 6) of the GTF2A1L gene. This alteration results from a C to T substitution at nucleotide position 611, causing the proline (P) at amino acid position 204 to be replaced by a leucine (L). 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