chr19-56177124-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.16G>A(p.Val6Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,016 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
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.16G>A | p.Val6Ile | missense_variant | 2/6 | ENST00000357330.7 | |
GALP | NM_001145546.2 | c.16G>A | p.Val6Ile | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALP | ENST00000357330.7 | c.16G>A | p.Val6Ile | missense_variant | 2/6 | 1 | NM_033106.4 | P2 | |
GALP | ENST00000590002.1 | c.16G>A | p.Val6Ile | missense_variant | 1/2 | 1 | A2 | ||
GALP | ENST00000440823.1 | c.16G>A | p.Val6Ile | missense_variant | 2/5 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250130Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135160
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461174Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 726880
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151842Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74122
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.16G>A (p.V6I) 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 16, causing the valine (V) at amino acid position 6 to be replaced by an isoleucine (I). 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