3-86966777-A-G

Position:

• chr3-86966777-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS1

The NM_016206.4(VGLL3):​c.937+1813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.011 (0 hom., cov: 0)
• Consequence: VGLL3 NM_016206.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

VGLL3 (HGNC:24327): (vestigial like family member 3) Predicted to enable protein C-terminus binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0108 (139/12892) while in subpopulation AFR AF= 0.0334 (99/2962). AF 95% confidence interval is 0.0281. There are 0 homozygotes in gnomad4. There are 67 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VGLL3	NM_016206.4	c.937+1813T>C		intron_variant		ENST00000398399.7
VGLL3	NM_001320493.2	c.937+1813T>C		intron_variant
VGLL3	NM_001320494.2	c.778+1813T>C		intron_variant
VGLL3	XM_006713138.5	c.934+1813T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VGLL3	ENST00000398399.7	c.937+1813T>C		intron_variant		1	NM_016206.4	P1
VGLL3	ENST00000383698.3	c.937+1813T>C		intron_variant		1
VGLL3	ENST00000637106.1	c.42+1813T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0108 AC: 139 AN: 12896 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00400

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00314

Gnomad FIN AF: 0.00136

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00489

Gnomad OTH AF: 0.00595

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0108 AC: 139 AN: 12892 Hom.: 0 Cov.: 0 AF XY: 0.0109 AC XY: 67 AN XY: 6124

Gnomad4 AFR AF: 0.0334

Gnomad4 AMR AF: 0.00399

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00325

Gnomad4 FIN AF: 0.00136

Gnomad4 NFE AF: 0.00490

Gnomad4 OTH AF: 0.00575

Alfa AF: 0.00253 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344083; hg19: chr3-87015927; COSMIC: COSV67354734; COSMIC: COSV67354734;