chr19-56180613-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_033106.4(GALP):c.115G>T(p.Ala39Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,852 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_033106.4 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 |
---|---|---|---|---|---|---|---|
GALP | NM_033106.4 | c.115G>T | p.Ala39Ser | missense_variant | 3/6 | ENST00000357330.7 | |
GALP | NM_001145546.2 | c.88-1559G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALP | ENST00000357330.7 | c.115G>T | p.Ala39Ser | missense_variant | 3/6 | 1 | NM_033106.4 | P2 | |
GALP | ENST00000590002.1 | c.88-1559G>T | intron_variant | 1 | A2 | ||||
GALP | ENST00000440823.1 | c.88-1559G>T | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251426Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135892
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461754Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 727194
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.115G>T (p.A39S) alteration is located in exon 3 (coding exon 2) of the GALP gene. This alteration results from a G to T substitution at nucleotide position 115, causing the alanine (A) at amino acid position 39 to be replaced by a serine (S). 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