7-101163337-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003378.4(VGF):c.1507G>A(p.Val503Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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. V503A) has been classified as Uncertain significance.
Frequency
Consequence
NM_003378.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGF | NM_003378.4 | c.1507G>A | p.Val503Ile | missense_variant | Exon 2 of 2 | ENST00000249330.3 | NP_003369.2 | |
VGF | XM_005250561.6 | c.1507G>A | p.Val503Ile | missense_variant | Exon 2 of 2 | XP_005250618.1 | ||
VGF | XM_011516549.4 | c.1507G>A | p.Val503Ile | missense_variant | Exon 3 of 3 | XP_011514851.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000554 AC: 6AN: 10828Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000128 AC: 1AN: 78386Hom.: 0 AF XY: 0.0000243 AC XY: 1AN XY: 41152
GnomAD4 exome AF: 0.0000336 AC: 8AN: 237800Hom.: 0 Cov.: 4 AF XY: 0.0000402 AC XY: 5AN XY: 124292
GnomAD4 genome AF: 0.000554 AC: 6AN: 10832Hom.: 0 Cov.: 0 AF XY: 0.000375 AC XY: 2AN XY: 5332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1507G>A (p.V503I) alteration is located in exon 2 (coding exon 1) of the VGF gene. This alteration results from a G to A substitution at nucleotide position 1507, causing the valine (V) at amino acid position 503 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