3-11652993-T-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.854
Variant links:
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
VGLL4NM_001284390.2 linkuse as main transcriptc.79+18269A>G intron_variant NP_001271319.1
VGLL4NM_014667.4 linkuse as main transcriptc.64+49978A>G intron_variant NP_055482.2
VGLL4XM_024453835.2 linkuse as main transcriptc.64+49978A>G intron_variant XP_024309603.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VGLL4ENST00000273038.7 linkuse as main transcriptc.64+49978A>G intron_variant 1 ENSP00000273038
VGLL4ENST00000426568.5 linkuse as main transcriptc.79+18269A>G intron_variant 1 ENSP00000413030
VGLL4ENST00000417206.6 linkuse as main transcriptc.64+49978A>G intron_variant 4 ENSP00000391932

Frequencies

GnomAD3 genomes
AF:
0.749
AC:
113878
AN:
151966
Hom.:
42801
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.798
Gnomad AMI
AF:
0.730
Gnomad AMR
AF:
0.783
Gnomad ASJ
AF:
0.686
Gnomad EAS
AF:
0.630
Gnomad SAS
AF:
0.655
Gnomad FIN
AF:
0.714
Gnomad MID
AF:
0.755
Gnomad NFE
AF:
0.737
Gnomad OTH
AF:
0.755
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.749
AC:
113980
AN:
152084
Hom.:
42847
Cov.:
32
AF XY:
0.749
AC XY:
55689
AN XY:
74326
show subpopulations
Gnomad4 AFR
AF:
0.798
Gnomad4 AMR
AF:
0.783
Gnomad4 ASJ
AF:
0.686
Gnomad4 EAS
AF:
0.630
Gnomad4 SAS
AF:
0.655
Gnomad4 FIN
AF:
0.714
Gnomad4 NFE
AF:
0.737
Gnomad4 OTH
AF:
0.752
Alfa
AF:
0.741
Hom.:
61313
Bravo
AF:
0.756
Asia WGS
AF:
0.678
AC:
2359
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.1
DANN
Benign
0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4684792; hg19: chr3-11694467; API