Genetic Variant VIPR1:c.79-2125A>G (chr3-42511624-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004624.4(VIPR1):c.79-2125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 151,886 control chromosomes in the GnomAD database, including 49,810 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 0.81 ( 49789 hom., cov: 32)

Exomes 𝑓: 0.90 ( 21 hom. )

Consequence

VIPR1
NM_004624.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Publications

2 publications found

Variant links:

Genes affected

VIPR1 (HGNC:12694): (vasoactive intestinal peptide receptor 1) 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. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

VIPR1 links:

VIPR1-AS1 (HGNC:40610): (VIPR1 antisense RNA 1)

VIPR1-AS1 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004624.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
VIPR1	NM_004624.4	MANE Select	c.79-2125A>G	intron	N/A	NP_004615.2
VIPR1	NM_001251885.2		c.15-2142A>G	intron	N/A	NP_001238814.1	B4DNY6
VIPR1	NM_001251882.2		c.-244-1127A>G	intron	N/A	NP_001238811.1	P32241-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
VIPR1	ENST00000325123.5	TSL:1 MANE Select	c.79-2125A>G	intron	N/A	ENSP00000327246.4	P32241-1
VIPR1	ENST00000883021.1		c.79-2125A>G	intron	N/A	ENSP00000553080.1
VIPR1	ENST00000883016.1		c.79-2125A>G	intron	N/A	ENSP00000553075.1

Frequencies

GnomAD3 genomes

AF:

0.809

AC:

122749

AN:

151714

Hom.:

49740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.862

Gnomad ASJ

AF:

0.812

Gnomad EAS

AF:

0.986

Gnomad SAS

AF:

0.839

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.796

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.833

GnomAD4 exome

AF:

0.904

AC:

AN:

Hom.:

AF XY:

0.875

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.875

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.933

AC:

AN:

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

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:

0.809

AC:

122857

AN:

151834

Hom.:

49789

Cov.:

AF XY:

0.809

AC XY:

60051

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.825

AC:

34139

AN:

41358

American (AMR)

AF:

0.862

AC:

13166

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.812

AC:

2818

AN:

3472

East Asian (EAS)

AF:

0.985

AC:

5094

AN:

5170

South Asian (SAS)

AF:

0.839

AC:

4044

AN:

4820

European-Finnish (FIN)

AF:

0.751

AC:

7922

AN:

10546

Middle Eastern (MID)

AF:

0.795

AC:

232

AN:

292

European-Non Finnish (NFE)

AF:

0.780

AC:

52978

AN:

67880

Other (OTH)

AF:

0.834

AC:

1762

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1216

2432

3647

4863

6079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

878

1756

2634

3512

4390

<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:

0.789

Hom.:

6749

Bravo

AF:

0.822

Asia WGS

AF:

0.914

AC:

3180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.84

(source)

DANN

Benign

0.58

PhyloP100

-1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over