7-101163358-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003378.4(VGF):c.1486G>T(p.Ala496Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 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. A496T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003378.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGF | NM_003378.4 | c.1486G>T | p.Ala496Ser | missense_variant | Exon 2 of 2 | ENST00000249330.3 | NP_003369.2 | |
VGF | XM_005250561.6 | c.1486G>T | p.Ala496Ser | missense_variant | Exon 2 of 2 | XP_005250618.1 | ||
VGF | XM_011516549.4 | c.1486G>T | p.Ala496Ser | missense_variant | Exon 3 of 3 | XP_011514851.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 18
GnomAD4 exome Cov.: 40
GnomAD4 genome Cov.: 18
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1486G>T (p.A496S) alteration is located in exon 2 (coding exon 1) of the VGF gene. This alteration results from a G to T substitution at nucleotide position 1486, causing the alanine (A) at amino acid position 496 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
Publications
No publications associated with this variant yet.