rs1344083

Variant names:

• chr3-86966777-A-G
• rs1344083
• NM_016206.4:c.937+1813T>C

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 rank	MANE	Protein	UniProt
VGLL3	NM_016206.4	c.937+1813T>C		intron_variant	Intron 3 of 3	ENST00000398399.7	NP_057290.2
VGLL3	NM_001320493.2	c.937+1813T>C		intron_variant	Intron 3 of 3		NP_001307422.1
VGLL3	NM_001320494.2	c.778+1813T>C		intron_variant	Intron 3 of 3		NP_001307423.1
VGLL3	XM_006713138.5	c.934+1813T>C		intron_variant	Intron 3 of 3		XP_006713201.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VGLL3	ENST00000398399.7	c.937+1813T>C		intron_variant	Intron 3 of 3	1	NM_016206.4	ENSP00000381436.2
VGLL3	ENST00000383698.3	c.937+1813T>C		intron_variant	Intron 3 of 3	1		ENSP00000373199.3
VGLL3	ENST00000637106.1	n.40+1813T>C		intron_variant	Intron 1 of 5	5		ENSP00000489678.1

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;