rs10923223

Variant names:

• chr1-117203951-C-A
• rs10923223
• NM_024626.4:c.32+6873G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-117203951-C-A
• chr1-117203951-C-G
• chr1-117203951-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_024626.4(VTCN1):​c.32+6873G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00152 in 210,346 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0015 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0015 (0 hom.)
• Consequence: VTCN1 NM_024626.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 9 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4	c.32+6873G>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.32+6873G>T		intron_variant	Intron 1 of 5	1	NM_024626.4	ENSP00000358470.3

Frequencies

GnomAD3 genomes AF: 0.00154 AC: 234 AN: 151996 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000339

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000852

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00557

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00212

Gnomad OTH AF: 0.000957

GnomAD4 exome AF: 0.00146 AC: 85 AN: 58232 Hom.: 0 AF XY: 0.00134 AC XY: 38 AN XY: 28378

African (AFR) AF: 0.00 AC: 0 AN: 992

American (AMR) AF: 0.00 AC: 0 AN: 68

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 356

East Asian (EAS) AF: 0.00 AC: 0 AN: 226

South Asian (SAS) AF: 0.00 AC: 0 AN: 1140

European-Finnish (FIN) AF: 0.0357 AC: 1 AN: 28

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 150

European-Non Finnish (NFE) AF: 0.00150 AC: 80 AN: 53344

Other (OTH) AF: 0.00207 AC: 4 AN: 1928

GnomAD4 genome AF: 0.00154 AC: 234 AN: 152114 Hom.: 0 Cov.: 31 AF XY: 0.00137 AC XY: 102 AN XY: 74376

African (AFR) AF: 0.000338 AC: 14 AN: 41434

American (AMR) AF: 0.000851 AC: 13 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00557 AC: 59 AN: 10598

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00212 AC: 144 AN: 68012

Other (OTH) AF: 0.000947 AC: 2 AN: 2112

Alfa AF: 0.0000903 Hom.: 7062

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.033
DANN	Benign	0.49
PhyloP100		-1.2
PromoterAI		-0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10923223; hg19: chr1-117746573;