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. The variant received -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
• Publications: 6 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=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024626.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VTCN1	NM_024626.4	MANE Select	c.*1401G>T		3_prime_UTR	Exon 6 of 6	NP_078902.2
	VTCN1	NR_045603.2		n.2412G>T		non_coding_transcript_exon	Exon 6 of 6
	VTCN1	NR_045604.2		n.2116G>T		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VTCN1	ENST00000369458.8	TSL:1 MANE Select	c.*1401G>T		3_prime_UTR	Exon 6 of 6	ENSP00000358470.3
	VTCN1	ENST00000359008.8	TSL:5	c.*1401G>T		3_prime_UTR	Exon 6 of 6	ENSP00000351899.4
	VTCN1	ENST00000539893.5	TSL:2	c.*1401G>T		3_prime_UTR	Exon 6 of 6	ENSP00000444724.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 10 AN: 12

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.813 AC: 33718 AN: 41498

American (AMR) AF: 0.788 AC: 12046 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2467 AN: 3470

East Asian (EAS) AF: 0.874 AC: 4510 AN: 5160

South Asian (SAS) AF: 0.708 AC: 3409 AN: 4814

European-Finnish (FIN) AF: 0.784 AC: 8290 AN: 10570

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48790 AN: 67988

Other (OTH) AF: 0.713 AC: 1509 AN: 2116

Alfa AF: 0.723 Hom.: 10376

Bravo AF: 0.762

Asia WGS AF: 0.781 AC: 2715 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	9.8
DANN	Benign	0.87
PhyloP100		1.5
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: rs13505; hg19: chr1-117686492;