dbSNP rs3738414: VTCN1:c.-51C>T (chr1-117210906-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024626.4(VTCN1):c.-51C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0226 in 1,600,222 control chromosomes in the GnomAD database, including 2,021 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 0.023 ( 221 hom., cov: 32)

Exomes 𝑓: 0.023 ( 1800 hom. )

Consequence

VTCN1
NM_024626.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.357

Publications

14 publications found

Variant links:

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]

VTCN1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VTCN1	NM_024626.4 link	c.-51C>T		5_prime_UTR_variant	Exon 1 of 6	ENST00000369458.8	NP_078902.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
VTCN1	ENST00000369458.8 link	c.-51C>T	5_prime_UTR_variant	Exon 1 of 6	1	NM_024626.4	ENSP00000358470.3	Q7Z7D3-1
VTCN1	ENST00000463461.5 link	n.22C>T	non_coding_transcript_exon_variant	Exon 1 of 4	3
VTCN1	ENST00000328189.7 link	c.-51C>T	5_prime_UTR_variant	Exon 1 of 5	5		ENSP00000328168.3	Q7Z7D3-2

Frequencies

GnomAD3 genomes

AF:

0.0227

AC:

3453

AN:

152164

Hom.:

221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00352

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0121

Gnomad ASJ

AF:

0.0153

Gnomad EAS

AF:

0.276

Gnomad SAS

AF:

0.0149

Gnomad FIN

AF:

0.0533

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0136

Gnomad OTH

AF:

0.0239

GnomAD2 exomes

AF:

0.0380

AC:

9551

AN:

251048

AF XY:

0.0355

show subpopulations

Gnomad AFR exome

AF:

0.00363

Gnomad AMR exome

AF:

0.0256

Gnomad ASJ exome

AF:

0.0152

Gnomad EAS exome

AF:

0.287

Gnomad FIN exome

AF:

0.0529

Gnomad NFE exome

AF:

0.0137

Gnomad OTH exome

AF:

0.0268

GnomAD4 exome

AF:

0.0226

AC:

32758

AN:

1447940

Hom.:

1800

Cov.:

AF XY:

0.0220

AC XY:

15869

AN XY:

721266

show subpopulations

African (AFR)

AF:

0.00295

AC:

AN:

33206

American (AMR)

AF:

0.0242

AC:

1082

AN:

44678

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

405

AN:

26030

East Asian (EAS)

AF:

0.273

AC:

10818

AN:

39644

South Asian (SAS)

AF:

0.00974

AC:

837

AN:

85906

European-Finnish (FIN)

AF:

0.0515

AC:

2747

AN:

53302

Middle Eastern (MID)

AF:

0.00583

AC:

AN:

5488

European-Non Finnish (NFE)

AF:

0.0135

AC:

14879

AN:

1099790

Other (OTH)

AF:

0.0311

AC:

1860

AN:

59896

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1525

3050

4576

6101

7626

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

714

1428

2142

2856

3570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0227

AC:

3450

AN:

152282

Hom.:

221

Cov.:

AF XY:

0.0260

AC XY:

1939

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.00351

AC:

146

AN:

41576

American (AMR)

AF:

0.0121

AC:

185

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0153

AC:

AN:

3470

East Asian (EAS)

AF:

0.277

AC:

1424

AN:

5148

South Asian (SAS)

AF:

0.0149

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.0533

AC:

566

AN:

10620

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0136

AC:

923

AN:

68016

Other (OTH)

AF:

0.0232

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

149

298

448

597

746

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0165

Hom.:

173

Bravo

AF:

0.0211

Asia WGS

AF:

0.0990

AC:

343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

9.5

(source)

DANN

Benign

0.76

PhyloP100

-0.36

PromoterAI

-0.16

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over