dbSNP rs7627240: VIPR1:c.79-3868C>T (chr3-42509881-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_004624.4(VIPR1):c.79-3868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,248 control chromosomes in the GnomAD database, including 9,044 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 0.31 ( 9032 hom., cov: 32)

Exomes 𝑓: 0.50 ( 12 hom. )

Consequence

VIPR1
NM_004624.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

6 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:

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 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
VIPR1	NM_004624.4	MANE Select	c.79-3868C>T	intron	N/A	NP_004615.2
VIPR1	NM_001251885.2		c.15-3885C>T	intron	N/A	NP_001238814.1
VIPR1	NM_001251882.2		c.-244-2870C>T	intron	N/A	NP_001238811.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
VIPR1	ENST00000325123.5	TSL:1 MANE Select	c.79-3868C>T	intron	N/A	ENSP00000327246.4
VIPR1	ENST00000433647.5	TSL:2	c.-244-2870C>T	intron	N/A	ENSP00000394950.1
VIPR1	ENST00000543411.5	TSL:2	c.43+7068C>T	intron	N/A	ENSP00000445701.1

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47749

AN:

152026

Hom.:

9029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.347

GnomAD4 exome

AF:

0.500

AC:

AN:

104

Hom.:

AF XY:

0.515

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.547

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.314

AC:

47769

AN:

152144

Hom.:

9032

Cov.:

AF XY:

0.316

AC XY:

23507

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.101

AC:

4204

AN:

41548

American (AMR)

AF:

0.406

AC:

6198

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.419

AC:

1454

AN:

3468

East Asian (EAS)

AF:

0.143

AC:

741

AN:

5168

South Asian (SAS)

AF:

0.254

AC:

1223

AN:

4818

European-Finnish (FIN)

AF:

0.463

AC:

4889

AN:

10562

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.410

AC:

27838

AN:

67980

Other (OTH)

AF:

0.344

AC:

726

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1566

3131

4697

6262

7828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.370

Hom.:

25068

Bravo

AF:

0.301

Asia WGS

AF:

0.226

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.26

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