1-117143870-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024626.4(VTCN1):​c.*1401G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).

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>C		3_prime_UTR	Exon 6 of 6	NP_078902.2
	VTCN1	NM_001253849.2		c.*1401G>C		3_prime_UTR	Exon 6 of 6	NP_001240778.1
	VTCN1	NM_001253850.2		c.*1401G>C		3_prime_UTR	Exon 5 of 5	NP_001240779.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VTCN1	ENST00000369458.8	TSL:1 MANE Select	c.*1401G>C		3_prime_UTR	Exon 6 of 6	ENSP00000358470.3
	VTCN1	ENST00000359008.8	TSL:5	c.*1401G>C		3_prime_UTR	Exon 6 of 6	ENSP00000351899.4
	VTCN1	ENST00000856907.1		c.*3788G>C		3_prime_UTR	Exon 5 of 5	ENSP00000526966.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 10376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.9
DANN	Benign	0.90
PhyloP100		1.5

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;