7-159054238-G-T

Variant names:

• chr7-159054238-G-T
• rs2730260
• NM_003382.5:c.455+4243C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003382.5(VIPR2):​c.455+4243C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,062 control chromosomes in the GnomAD database, including 40,326 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 0.72 (40326 hom., cov: 33)
• Consequence: VIPR2 NM_003382.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 18 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.787 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR2	NM_003382.5	MANE Select	c.455+4243C>A		intron	N/A	NP_003373.2
	VIPR2	NM_001308259.1		c.407+4243C>A		intron	N/A	NP_001295188.1	P41587-2
	VIPR2	NM_001304522.2		c.358-17336C>A		intron	N/A	NP_001291451.1	X5DP12

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR2	ENST00000262178.7	TSL:1 MANE Select	c.455+4243C>A		intron	N/A	ENSP00000262178.2	P41587-1
	VIPR2	ENST00000402066.5	TSL:5	c.878+4243C>A		intron	N/A	ENSP00000384497.1	C9JCP7
	VIPR2	ENST00000958129.1		c.878+4243C>A		intron	N/A	ENSP00000628188.1

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109228 AN: 151944 Hom.: 40320 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.719 AC: 109268 AN: 152062 Hom.: 40326 Cov.: 33 AF XY: 0.723 AC XY: 53727 AN XY: 74352

African (AFR) AF: 0.527 AC: 21831 AN: 41432

American (AMR) AF: 0.799 AC: 12210 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2930 AN: 3472

East Asian (EAS) AF: 0.773 AC: 3993 AN: 5168

South Asian (SAS) AF: 0.795 AC: 3828 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8380 AN: 10568

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53662 AN: 68004

Other (OTH) AF: 0.774 AC: 1633 AN: 2110

Alfa AF: 0.773 Hom.: 198942

Bravo AF: 0.710

Asia WGS AF: 0.792 AC: 2754 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	9.6
DANN	Benign	0.74
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2730260; hg19: chr7-158846929;