chr19-56177187-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033106.4(GALP):c.79G>A(p.Ala27Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,972 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. A27V) has been classified as Likely benign.
Frequency
Consequence
NM_033106.4 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 |
---|---|---|---|---|---|---|---|
GALP | NM_033106.4 | c.79G>A | p.Ala27Thr | missense_variant | 2/6 | ENST00000357330.7 | |
GALP | NM_001145546.2 | c.79G>A | p.Ala27Thr | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALP | ENST00000357330.7 | c.79G>A | p.Ala27Thr | missense_variant | 2/6 | 1 | NM_033106.4 | P2 | |
GALP | ENST00000590002.1 | c.79G>A | p.Ala27Thr | missense_variant | 1/2 | 1 | A2 | ||
GALP | ENST00000440823.1 | c.79G>A | p.Ala27Thr | missense_variant | 2/5 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151930Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461042Hom.: 1 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726892
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151930Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74178
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.79G>A (p.A27T) alteration is located in exon 2 (coding exon 1) of the GALP gene. This alteration results from a G to A substitution at nucleotide position 79, causing the alanine (A) at amino acid position 27 to be replaced by a threonine (T). 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