19-12748013-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004317.4(GET3):c.956C>T(p.Pro319Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000206 in 1,459,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004317.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GET3 | NM_004317.4 | c.956C>T | p.Pro319Leu | missense_variant | Exon 7 of 7 | ENST00000357332.8 | NP_004308.2 | |
GET3 | NM_001371488.1 | c.956C>T | p.Pro319Leu | missense_variant | Exon 8 of 8 | NP_001358417.1 | ||
GET3 | NM_001371489.1 | c.956C>T | p.Pro319Leu | missense_variant | Exon 8 of 8 | NP_001358418.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250284Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135244
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1459338Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 725680
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.956C>T (p.P319L) alteration is located in exon 7 (coding exon 7) of the ASNA1 gene. This alteration results from a C to T substitution at nucleotide position 956, causing the proline (P) at amino acid position 319 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