NM_024626.4:c.*1901T>C

Variant names:

• chr1-117143370-A-G
• rs6673837
• NM_024626.4:c.*1901T>C

Variant summary

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

The NM_024626.4(VTCN1):​c.*1901T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,218 control chromosomes in the GnomAD database, including 55,607 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 0.85 (55607 hom., cov: 32)
• Consequence: VTCN1 NM_024626.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 4 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]

LOC124904387 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.*1901T>C		downstream_gene_variant		ENST00000369458.8	NP_078902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VTCN1	ENST00000369458.8	c.*1901T>C		downstream_gene_variant		1	NM_024626.4	ENSP00000358470.3
VTCN1	ENST00000359008.8	c.*1901T>C		downstream_gene_variant		5		ENSP00000351899.4
VTCN1	ENST00000539893.5	c.*1901T>C		downstream_gene_variant		2		ENSP00000444724.1
VTCN1	ENST00000328189.7	c.*1901T>C		downstream_gene_variant		5		ENSP00000328168.3

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129557 AN: 152100 Hom.: 55554 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.852 AC: 129671 AN: 152218 Hom.: 55607 Cov.: 32 AF XY: 0.853 AC XY: 63500 AN XY: 74408

African (AFR) AF: 0.943 AC: 39199 AN: 41552

American (AMR) AF: 0.864 AC: 13211 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3470

East Asian (EAS) AF: 0.977 AC: 5060 AN: 5178

South Asian (SAS) AF: 0.831 AC: 4005 AN: 4820

European-Finnish (FIN) AF: 0.825 AC: 8726 AN: 10582

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54092 AN: 68002

Other (OTH) AF: 0.813 AC: 1717 AN: 2112

Alfa AF: 0.839 Hom.: 9951

Bravo AF: 0.857

Asia WGS AF: 0.911 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6673837; hg19: chr1-117685992;