1-117187426-G-C

Variant names:

• chr1-117187426-G-C
• rs10923217
• NM_024626.4:c.33-17255C>G

Variant summary

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

The NM_024626.4(VTCN1):​c.33-17255C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,760 control chromosomes in the GnomAD database, including 19,426 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 0.49 (19426 hom., cov: 30)
• Consequence: VTCN1 NM_024626.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.33-17255C>G		intron_variant	Intron 1 of 5	ENST00000369458.8	NP_078902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VTCN1	ENST00000369458.8	c.33-17255C>G		intron_variant	Intron 1 of 5	1	NM_024626.4	ENSP00000358470.3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74454 AN: 151646 Hom.: 19413 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.491 AC: 74495 AN: 151760 Hom.: 19426 Cov.: 30 AF XY: 0.502 AC XY: 37202 AN XY: 74142

African (AFR) AF: 0.331 AC: 13676 AN: 41324

American (AMR) AF: 0.589 AC: 8979 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4264 AN: 5174

South Asian (SAS) AF: 0.637 AC: 3058 AN: 4804

European-Finnish (FIN) AF: 0.612 AC: 6437 AN: 10518

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34809 AN: 67908

Other (OTH) AF: 0.494 AC: 1042 AN: 2108

Alfa AF: 0.494 Hom.: 2320

Bravo AF: 0.481

Asia WGS AF: 0.691 AC: 2402 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	0.72
DANN	Benign	0.46
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10923217; hg19: chr1-117730048;