chr3-86968650-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016206.4(VGLL3):c.877G>A(p.Ala293Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,880 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016206.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGLL3 | NM_016206.4 | c.877G>A | p.Ala293Thr | missense_variant | Exon 3 of 4 | ENST00000398399.7 | NP_057290.2 | |
VGLL3 | NM_001320493.2 | c.877G>A | p.Ala293Thr | missense_variant | Exon 3 of 4 | NP_001307422.1 | ||
VGLL3 | NM_001320494.2 | c.718G>A | p.Ala240Thr | missense_variant | Exon 3 of 4 | NP_001307423.1 | ||
VGLL3 | XM_006713138.5 | c.874G>A | p.Ala292Thr | missense_variant | Exon 3 of 4 | XP_006713201.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VGLL3 | ENST00000398399.7 | c.877G>A | p.Ala293Thr | missense_variant | Exon 3 of 4 | 1 | NM_016206.4 | ENSP00000381436.2 | ||
VGLL3 | ENST00000383698.3 | c.877G>A | p.Ala293Thr | missense_variant | Exon 3 of 4 | 1 | ENSP00000373199.3 | |||
VGLL3 | ENST00000494229.1 | c.*53G>A | downstream_gene_variant | 3 | ENSP00000419115.1 | |||||
VGLL3 | ENST00000637106.1 | n.-21G>A | upstream_gene_variant | 5 | ENSP00000489678.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249350Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135282
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727238
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.877G>A (p.A293T) alteration is located in exon 3 (coding exon 3) of the VGLL3 gene. This alteration results from a G to A substitution at nucleotide position 877, causing the alanine (A) at amino acid position 293 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