3-42536843-T-C

Variant names:

• chr3-42536843-T-C
• rs896
• NM_004624.4:c.*562T>C

Variant summary

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

The NM_004624.4(VIPR1):​c.*562T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,150 control chromosomes in the GnomAD database, including 32,574 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 0.64 (32574 hom., cov: 33)
  • Exomes 𝑓: 0.50 (8 hom.)
  • Failed GnomAD Quality Control
• Consequence: VIPR1 NM_004624.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 12 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	NM_004624.4	MANE Select	c.*562T>C		3_prime_UTR	Exon 13 of 13	NP_004615.2
	VIPR1	NM_001251885.2		c.*562T>C		3_prime_UTR	Exon 13 of 13	NP_001238814.1
	VIPR1	NM_001251882.2		c.*562T>C		3_prime_UTR	Exon 14 of 14	NP_001238811.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	VIPR1	ENST00000325123.5	TSL:1 MANE Select	c.*562T>C		3_prime_UTR	Exon 13 of 13	ENSP00000327246.4
	VIPR1	ENST00000498102.1	TSL:2	n.3035T>C		non_coding_transcript_exon	Exon 3 of 3
	VIPR1	ENST00000433647.5	TSL:2	c.*562T>C		3_prime_UTR	Exon 14 of 14	ENSP00000394950.1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97780 AN: 152034 Hom.: 32541 Cov.: 33

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.635

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.500 AC: 34 AN: 68 Hom.: 8 Cov.: 0 AF XY: 0.447 AC XY: 17 AN XY: 38

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.480 AC: 24 AN: 50

Other (OTH) AF: 0.500 AC: 4 AN: 8

GnomAD4 genome AF: 0.643 AC: 97863 AN: 152150 Hom.: 32574 Cov.: 33 AF XY: 0.644 AC XY: 47930 AN XY: 74372

African (AFR) AF: 0.817 AC: 33926 AN: 41538

American (AMR) AF: 0.576 AC: 8810 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3468

East Asian (EAS) AF: 0.769 AC: 3976 AN: 5172

South Asian (SAS) AF: 0.688 AC: 3318 AN: 4824

European-Finnish (FIN) AF: 0.577 AC: 6105 AN: 10584

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37548 AN: 67970

Other (OTH) AF: 0.634 AC: 1335 AN: 2106

Alfa AF: 0.614 Hom.: 7243

Bravo AF: 0.651

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.56
PhyloP100		-0.070
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: rs896; hg19: chr3-42578335;