dbSNP rs688136: VIP:c.*60T>C (chr6-152758926-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003381.4(VIP):c.*60T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,158 control chromosomes in the GnomAD database, including 13,436 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 0.41 ( 13422 hom., cov: 33)

Exomes 𝑓: 0.35 ( 14 hom. )

Consequence

VIP
NM_003381.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

12 publications found

Variant links:

Genes affected

VIP (HGNC:12693): (vasoactive intestinal peptide) The protein encoded by this gene belongs to the glucagon family. It stimulates myocardial contractility, causes vasodilation, increases glycogenolysis, lowers arterial blood pressure and relaxes the smooth muscle of trachea, stomach and gall bladder. The protein also acts as an antimicrobial peptide with antibacterial and antifungal activity. Alternative splicing occurs at this locus and two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Nov 2014]

VIP links:

LINC02840 (HGNC:54374): (long intergenic non-protein coding RNA 2840)

LINC02840 links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
VIP	NM_003381.4 link	c.*60T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000367244.8	NP_003372.1	P01282-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIP	ENST00000367244.8 link	c.*60T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_003381.4	ENSP00000356213.3		P01282-1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62081

AN:

151760

Hom.:

13396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.352

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.376

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.392

GnomAD4 exome

AF:

0.355

AC:

100

AN:

282

Hom.:

Cov.:

AF XY:

0.335

AC XY:

AN XY:

164

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.356

AC:

AN:

278

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.409

AC:

62150

AN:

151876

Hom.:

13422

Cov.:

AF XY:

0.406

AC XY:

30149

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.556

AC:

23042

AN:

41428

American (AMR)

AF:

0.323

AC:

4917

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

1300

AN:

3460

East Asian (EAS)

AF:

0.151

AC:

781

AN:

5166

South Asian (SAS)

AF:

0.360

AC:

1736

AN:

4826

European-Finnish (FIN)

AF:

0.375

AC:

3972

AN:

10578

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.370

AC:

25123

AN:

67882

Other (OTH)

AF:

0.390

AC:

823

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1880

3760

5640

7520

9400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

588

1176

1764

2352

2940

<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:

0.375

Hom.:

18140

Bravo

AF:

0.412

Asia WGS

AF:

0.262

AC:

912

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.020

(source)

DANN

Benign

0.52

PhyloP100

-1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over