1-117179558-G-T

Position:

• chr1-117179558-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024626.4(VTCN1):​c.33-9387C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,192 control chromosomes in the GnomAD database, including 47,689 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 0.78 (47689 hom., cov: 32)
• Consequence: VTCN1 NM_024626.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

VTCN1 (HGNC:28873): (V-set domain containing T cell activation inhibitor 1) This gene encodes a protein belonging to the B7 costimulatory protein family. Proteins in this family are present on the surface of antigen-presenting cells and interact with ligand bound to receptors on the surface of T cells. Studies have shown that high levels of the encoded protein has been correlated with tumor progression. A pseudogene of this gene is located on chromosome 20. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

VTCN1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.33-9387C>A		intron_variant		ENST00000369458.8	NP_078902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VTCN1	ENST00000369458.8	c.33-9387C>A		intron_variant		1	NM_024626.4	ENSP00000358470.3

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119124 AN: 152074 Hom.: 47635 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.783 AC: 119236 AN: 152192 Hom.: 47689 Cov.: 32 AF XY: 0.787 AC XY: 58537 AN XY: 74412

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.746

Alfa AF: 0.724 Hom.: 18799

Bravo AF: 0.792

Asia WGS AF: 0.916 AC: 3183 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	0.86
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4376721; hg19: chr1-117722180;