1-117179265-C-A

Variant names:

• chr1-117179265-C-A
• rs10801935
• NM_024626.4:c.33-9094G>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.33-9094G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,044 control chromosomes in the GnomAD database, including 25,663 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 0.57 (25663 hom., cov: 32)
• Consequence: VTCN1 NM_024626.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 11 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.33-9094G>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.33-9094G>T		intron_variant	Intron 1 of 5	1	NM_024626.4	ENSP00000358470.3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85877 AN: 151926 Hom.: 25650 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.565 AC: 85920 AN: 152044 Hom.: 25663 Cov.: 32 AF XY: 0.572 AC XY: 42516 AN XY: 74328

African (AFR) AF: 0.356 AC: 14742 AN: 41448

American (AMR) AF: 0.653 AC: 9985 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2072 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4182 AN: 5172

South Asian (SAS) AF: 0.663 AC: 3195 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7329 AN: 10556

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42676 AN: 67976

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.589 Hom.: 10311

Bravo AF: 0.552

Asia WGS AF: 0.698 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.70
PhyloP100		0.59
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: rs10801935; hg19: chr1-117721887;