6-117270890-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182645.3(VGLL2):c.739G>A(p.Ala247Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000179 in 1,283,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182645.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGLL2 | NM_182645.3 | c.739G>A | p.Ala247Thr | missense_variant | 3/4 | ENST00000326274.6 | NP_872586.1 | |
VGLL2 | XM_005266883.3 | c.739G>A | p.Ala247Thr | missense_variant | 3/4 | XP_005266940.1 | ||
VGLL2 | NM_153453.1 | c.392-1564G>A | intron_variant | NP_703154.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VGLL2 | ENST00000326274.6 | c.739G>A | p.Ala247Thr | missense_variant | 3/4 | 1 | NM_182645.3 | ENSP00000320957 | P4 | |
VGLL2 | ENST00000352536.7 | c.392-1564G>A | intron_variant | 1 | ENSP00000305405 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000398 AC: 6AN: 150888Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000150 AC: 17AN: 1132164Hom.: 0 Cov.: 31 AF XY: 0.0000164 AC XY: 9AN XY: 548850
GnomAD4 genome AF: 0.0000398 AC: 6AN: 150888Hom.: 0 Cov.: 31 AF XY: 0.0000272 AC XY: 2AN XY: 73664
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.739G>A (p.A247T) alteration is located in exon 3 (coding exon 3) of the VGLL2 gene. This alteration results from a G to A substitution at nucleotide position 739, causing the alanine (A) at amino acid position 247 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