3-11652993-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000426568.5(VGLL4):c.79+18269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,084 control chromosomes in the GnomAD database, including 42,847 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.75 ( 42847 hom., cov: 32)
Consequence
VGLL4
ENST00000426568.5 intron
ENST00000426568.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.854
Genes affected
VGLL4 (HGNC:28966): (vestigial like family member 4) Predicted to enable transcription coactivator binding activity. Involved in negative regulation of Wnt signaling pathway; negative regulation of cell growth; and negative regulation of hippo signaling. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VGLL4 | NM_001284390.2 | c.79+18269A>G | intron_variant | NP_001271319.1 | ||||
VGLL4 | NM_014667.4 | c.64+49978A>G | intron_variant | NP_055482.2 | ||||
VGLL4 | XM_024453835.2 | c.64+49978A>G | intron_variant | XP_024309603.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VGLL4 | ENST00000273038.7 | c.64+49978A>G | intron_variant | 1 | ENSP00000273038 | |||||
VGLL4 | ENST00000426568.5 | c.79+18269A>G | intron_variant | 1 | ENSP00000413030 | |||||
VGLL4 | ENST00000417206.6 | c.64+49978A>G | intron_variant | 4 | ENSP00000391932 |
Frequencies
GnomAD3 genomes AF: 0.749 AC: 113878AN: 151966Hom.: 42801 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.749 AC: 113980AN: 152084Hom.: 42847 Cov.: 32 AF XY: 0.749 AC XY: 55689AN XY: 74326
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at