rs13505

Variant names:

• chr1-117143870-C-A
• rs13505
• NM_024626.4:c.*1401G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-117143870-C-A
• chr1-117143870-C-G

Variant summary

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

The NM_024626.4(VTCN1):​c.*1401G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,128 control chromosomes in the GnomAD database, including 44,146 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 (44141 hom., cov: 32)
  • Exomes 𝑓: 0.86 (5 hom.)
• Consequence: VTCN1 NM_024626.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.*1401G>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000369458.8	NP_078902.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VTCN1	ENST00000369458	c.*1401G>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_024626.4	ENSP00000358470.3
VTCN1	ENST00000359008	c.*1401G>T		3_prime_UTR_variant	Exon 6 of 6	5		ENSP00000351899.4
VTCN1	ENST00000539893	c.*1401G>T		3_prime_UTR_variant	Exon 6 of 6	2		ENSP00000444724.1
VTCN1	ENST00000328189	c.*1401G>T		3_prime_UTR_variant	Exon 5 of 5	5		ENSP00000328168.3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115545 AN: 151996 Hom.: 44100 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.717

GnomAD4 exome AF: 0.857 AC: 12 AN: 14 Hom.: 5 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.760 AC: 115643 AN: 152114 Hom.: 44141 Cov.: 32 AF XY: 0.764 AC XY: 56834 AN XY: 74352

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.713

Alfa AF: 0.714 Hom.: 4587

Bravo AF: 0.762

Asia WGS AF: 0.781 AC: 2715 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13505; hg19: chr1-117686492;