chr1-117188001-G-A

Variant names:

• chr1-117188001-G-A
• rs6669320
• NM_024626.4:c.33-17830C>T

Variant summary

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

The NM_024626.4(VTCN1):​c.33-17830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,054 control chromosomes in the GnomAD database, including 1,872 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 0.15 (1872 hom., cov: 32)
• Consequence: VTCN1 NM_024626.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.33-17830C>T		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.33-17830C>T		intron_variant	Intron 1 of 5	1	NM_024626.4	ENSP00000358470.3

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22664 AN: 151936 Hom.: 1869 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.149 AC: 22684 AN: 152054 Hom.: 1872 Cov.: 32 AF XY: 0.144 AC XY: 10692 AN XY: 74324

African (AFR) AF: 0.214 AC: 8874 AN: 41416

American (AMR) AF: 0.117 AC: 1782 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5178

South Asian (SAS) AF: 0.101 AC: 489 AN: 4818

European-Finnish (FIN) AF: 0.0798 AC: 845 AN: 10586

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.143 AC: 9741 AN: 68004

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.139 Hom.: 534

Bravo AF: 0.155

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.55
PhyloP100		-0.092
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: rs6669320; hg19: chr1-117730623;