1-117203951-C-T

Position:

• chr1-117203951-C-T

Variant summary

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

The ENST00000369458.8(VTCN1):​c.32+6873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 210,140 control chromosomes in the GnomAD database, including 64,459 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 0.76 (44605 hom., cov: 31)
  • Exomes 𝑓: 0.82 (19854 hom.)
• Consequence: VTCN1 ENST00000369458.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.32+6873G>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.32+6873G>A		intron_variant		1	NM_024626.4	ENSP00000358470	P1
VTCN1	ENST00000328189.7	c.32+6873G>A		intron_variant		5		ENSP00000328168
VTCN1	ENST00000463461.5	n.104+6873G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115345 AN: 151948 Hom.: 44580 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.764

GnomAD4 exome AF: 0.824 AC: 47846 AN: 58074 Hom.: 19854 AF XY: 0.824 AC XY: 23319 AN XY: 28300

Gnomad4 AFR exome AF: 0.597

Gnomad4 AMR exome AF: 0.706

Gnomad4 ASJ exome AF: 0.772

Gnomad4 EAS exome AF: 0.558

Gnomad4 SAS exome AF: 0.703

Gnomad4 FIN exome AF: 0.821

Gnomad4 NFE exome AF: 0.835

Gnomad4 OTH exome AF: 0.765

GnomAD4 genome AF: 0.759 AC: 115409 AN: 152066 Hom.: 44605 Cov.: 31 AF XY: 0.758 AC XY: 56385 AN XY: 74346

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.767

Alfa AF: 0.780 Hom.: 7062

Bravo AF: 0.745

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.040
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10923223; hg19: chr1-117746573;