Genetic Variant VIPR2:c.*2338G>A (chr7-159028278-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_003382.5(VIPR2):c.*2338G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 154,596 control chromosomes in the GnomAD database, including 17,195 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 0.44 ( 16852 hom., cov: 35)

Exomes 𝑓: 0.51 ( 343 hom. )

Consequence

VIPR2
NM_003382.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

17 publications found

Variant links:

Genes affected

VIPR2 (HGNC:12695): (vasoactive intestinal peptide receptor 2) This gene encodes a receptor for vasoactive intestinal peptide, a small neuropeptide. Vasoactive intestinal peptide is involved in smooth muscle relaxation, exocrine and endocrine secretion, and water and ion flux in lung and intestinal epithelia. Its actions are effected through integral membrane receptors associated with a guanine nucleotide binding protein which activates adenylate cyclase. [provided by RefSeq, Aug 2011]

VIPR2 links:

LINC00689 (HGNC:27217): (long intergenic non-protein coding RNA 689)

LINC00689 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_003382.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003382.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
VIPR2	NM_003382.5	MANE Select	c.*2338G>A	3_prime_UTR	Exon 13 of 13	NP_003373.2
VIPR2	NM_001308259.1		c.*2338G>A	3_prime_UTR	Exon 10 of 10	NP_001295188.1	P41587-2
VIPR2	NM_001304522.2		c.*2338G>A	3_prime_UTR	Exon 11 of 11	NP_001291451.1	X5DP12

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
VIPR2	ENST00000262178.7	TSL:1 MANE Select	c.*2338G>A	3_prime_UTR	Exon 13 of 13	ENSP00000262178.2	P41587-1
LINC00689	ENST00000413238.2	TSL:1	n.4065C>T	non_coding_transcript_exon	Exon 6 of 6
VIPR2	ENST00000958129.1		c.*2338G>A	3_prime_UTR	Exon 11 of 11	ENSP00000628188.1

Frequencies

GnomAD3 genomes

AF:

0.436

AC:

66372

AN:

152062

Hom.:

16838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.575

Gnomad EAS

AF:

0.172

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.579

Gnomad OTH

AF:

0.464

GnomAD4 exome

AF:

0.510

AC:

1231

AN:

2416

Hom.:

343

Cov.:

AF XY:

0.511

AC XY:

639

AN XY:

1250

show subpopulations

African (AFR)

AF:

0.150

AC:

AN:

American (AMR)

AF:

0.587

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.518

AC:

AN:

East Asian (EAS)

AF:

0.174

AC:

AN:

224

South Asian (SAS)

AF:

0.467

AC:

AN:

European-Finnish (FIN)

AF:

0.492

AC:

195

AN:

396

Middle Eastern (MID)

AF:

0.455

AC:

AN:

European-Non Finnish (NFE)

AF:

0.581

AC:

839

AN:

1444

Other (OTH)

AF:

0.500

AC:

AN:

138

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

102

127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.436

AC:

66411

AN:

152180

Hom.:

16852

Cov.:

AF XY:

0.429

AC XY:

31880

AN XY:

74392

show subpopulations

African (AFR)

AF:

0.186

AC:

7709

AN:

41538

American (AMR)

AF:

0.498

AC:

7617

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.575

AC:

1996

AN:

3472

East Asian (EAS)

AF:

0.172

AC:

892

AN:

5172

South Asian (SAS)

AF:

0.429

AC:

2070

AN:

4824

European-Finnish (FIN)

AF:

0.493

AC:

5218

AN:

10582

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.579

AC:

39354

AN:

67968

Other (OTH)

AF:

0.465

AC:

982

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1746

3492

5239

6985

8731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<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:

0.519

Hom.:

31442

Bravo

AF:

0.429

Asia WGS

AF:

0.296

AC:

1035

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.5

(source)

DANN

Benign

0.70

PhyloP100

-0.0070

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over