rs17023661

Variant names:

• chr3-86919359-C-T
• rs17023661
• ENST00000637106.1:n.*15-10301G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637106.1(VGLL3):​n.*15-10301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0824 in 152,150 control chromosomes in the GnomAD database, including 1,106 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 0.082 (1106 hom., cov: 32)
• Consequence: VGLL3 ENST00000637106.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 6 publications found

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]

LOC105377196 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637106.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VGLL3	ENST00000637106.1	TSL:5	n.*15-10301G>A		intron	N/A	ENSP00000489678.1

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12504 AN: 152032 Hom.: 1099 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00651

Gnomad OTH AF: 0.0755

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

GnomAD4 genome AF: 0.0824 AC: 12530 AN: 152150 Hom.: 1106 Cov.: 32 AF XY: 0.0853 AC XY: 6344 AN XY: 74390

African (AFR) AF: 0.190 AC: 7869 AN: 41490

American (AMR) AF: 0.170 AC: 2598 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.180 AC: 931 AN: 5176

South Asian (SAS) AF: 0.0376 AC: 181 AN: 4818

European-Finnish (FIN) AF: 0.0253 AC: 268 AN: 10588

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00651 AC: 443 AN: 68018

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0460 Hom.: 1409

Bravo AF: 0.100

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.74
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17023661; hg19: chr3-86968509;