rs885863

Variant names:

• chr7-159028278-C-G
• rs885863
• ENST00000413238.2:n.4065C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-159028278-C-G
• chr7-159028278-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000413238.2(LINC00689):​n.4065C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 35)
• Consequence: LINC00689 ENST00000413238.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 17 publications found

Genes affected

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

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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413238.2. 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
	VIPR2	NM_003382.5	MANE Select	c.*2338G>C		3_prime_UTR	Exon 13 of 13	NP_003373.2
	VIPR2	NR_130758.2		n.4085G>C		non_coding_transcript_exon	Exon 13 of 13
	VIPR2	NM_001308259.1		c.*2338G>C		3_prime_UTR	Exon 10 of 10	NP_001295188.1

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		-0.0070

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: rs885863; hg19: chr7-158820969;