chr13-27435165-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002097.3(GTF3A):c.906T>A(p.Asp302Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000345 in 1,448,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D302G) has been classified as Uncertain significance.
Frequency
Consequence
NM_002097.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GTF3A | NM_002097.3 | c.906T>A | p.Asp302Glu | missense_variant | 8/9 | ENST00000381140.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GTF3A | ENST00000381140.10 | c.906T>A | p.Asp302Glu | missense_variant | 8/9 | 1 | NM_002097.3 | P1 | |
GTF3A | ENST00000419181.5 | c.*265T>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 | 1 | ||||
GTF3A | ENST00000470606.5 | n.1636T>A | non_coding_transcript_exon_variant | 8/9 | 2 | ||||
GTF3A | ENST00000482655.2 | n.411T>A | non_coding_transcript_exon_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000213 AC: 5AN: 234782Hom.: 0 AF XY: 0.0000157 AC XY: 2AN XY: 127566
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1448352Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 2AN XY: 720202
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.906T>A (p.D302E) alteration is located in exon 8 (coding exon 8) of the GTF3A gene. This alteration results from a T to A substitution at nucleotide position 906, causing the aspartic acid (D) at amino acid position 302 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