Genetic Variant VIP:c.107+903C>T (chr6-152753187-C-T) – 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.107+903C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 151,922 control chromosomes in the GnomAD database, including 7,874 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 0.28 ( 7874 hom., cov: 32)

Consequence

VIP
NM_003381.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.35

Publications

13 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 Gene-Disease associations (from GenCC):

Asperger syndrome
Inheritance: AD Classification: LIMITED Submitted by: G2P

VIP 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 = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
VIP	NM_003381.4 link	c.107+903C>T	intron_variant	Intron 2 of 6	ENST00000367244.8	NP_003372.1	P01282-1
VIP	NM_194435.3 link	c.107+903C>T	intron_variant	Intron 2 of 6		NP_919416.1	P01282-2
VIP	XM_006715562.5 link	c.107+903C>T	intron_variant	Intron 2 of 6		XP_006715625.1
VIP	XM_005267135.4 link	c.107+903C>T	intron_variant	Intron 2 of 6		XP_005267192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
VIP	ENST00000367244.8 link	c.107+903C>T		intron_variant	Intron 2 of 6	1	NM_003381.4	ENSP00000356213.3		P01282-1
VIP	ENST00000367243.7 link	c.107+903C>T		intron_variant	Intron 2 of 6	1		ENSP00000356212.3		P01282-2

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42627

AN:

151802

Hom.:

7840

Cov.:

show subpopulations

Gnomad AFR

AF:

0.524

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.201

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.0934

Gnomad SAS

AF:

0.215

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.284

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.281

AC:

42709

AN:

151922

Hom.:

7874

Cov.:

AF XY:

0.277

AC XY:

20592

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.525

AC:

21724

AN:

41410

American (AMR)

AF:

0.200

AC:

3052

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.296

AC:

1027

AN:

3468

East Asian (EAS)

AF:

0.0934

AC:

482

AN:

5162

South Asian (SAS)

AF:

0.216

AC:

1041

AN:

4822

European-Finnish (FIN)

AF:

0.189

AC:

1999

AN:

10566

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.184

AC:

12498

AN:

67950

Other (OTH)

AF:

0.282

AC:

594

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1401

2802

4204

5605

7006

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.215

Hom.:

18662

Bravo

AF:

0.292

Asia WGS

AF:

0.184

AC:

642

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

0.032

(source)

DANN

Benign

0.43

PhyloP100

-2.4

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