dbSNP rs885861: LINC00689:n.4643G>A (chr7-159028856-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000413238.2(LINC00689):n.4643G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 150,960 control chromosomes in the GnomAD database, including 16,399 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 0.43 ( 16372 hom., cov: 34)

Exomes 𝑓: 0.51 ( 27 hom. )

Consequence

LINC00689
ENST00000413238.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.369

Publications

15 publications found

Variant links:

Genes affected

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

LINC00689 links:

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]

VIPR2 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
VIPR2	NM_003382.5 link	c.*1760C>T	3_prime_UTR_variant	Exon 13 of 13	ENST00000262178.7	NP_003373.2	P41587-1X5D7Q6
VIPR2	NR_130758.2 link	n.3507C>T	non_coding_transcript_exon_variant	Exon 13 of 13
VIPR2	NM_001308259.1 link	c.*1760C>T	3_prime_UTR_variant	Exon 10 of 10		NP_001295188.1	P41587-2
VIPR2	NM_001304522.2 link	c.*1760C>T	3_prime_UTR_variant	Exon 11 of 11		NP_001291451.1	P41587X5DP12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00689	ENST00000413238.2 link	n.4643G>A		non_coding_transcript_exon_variant	Exon 6 of 6	1
VIPR2	ENST00000262178.7 link	c.*1760C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_003382.5	ENSP00000262178.2		P41587-1

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64260

AN:

150646

Hom.:

16356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.500

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.575

Gnomad OTH

AF:

0.456

GnomAD4 exome

AF:

0.505

AC:

101

AN:

200

Hom.:

Cov.:

AF XY:

0.465

AC XY:

AN XY:

144

show subpopulations

African (AFR)

AF:

0.200

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.375

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.524

AC:

AN:

164

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.426

AC:

64293

AN:

150760

Hom.:

16372

Cov.:

AF XY:

0.420

AC XY:

30946

AN XY:

73702

show subpopulations

African (AFR)

AF:

0.150

AC:

6046

AN:

40202

American (AMR)

AF:

0.490

AC:

7480

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.574

AC:

1992

AN:

3468

East Asian (EAS)

AF:

0.153

AC:

790

AN:

5160

South Asian (SAS)

AF:

0.430

AC:

2072

AN:

4818

European-Finnish (FIN)

AF:

0.500

AC:

5279

AN:

10566

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.575

AC:

39099

AN:

67984

Other (OTH)

AF:

0.457

AC:

961

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1709

3417

5126

6834

8543

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.537

Hom.:

26898

Bravo

AF:

0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.4

(source)

DANN

Benign

0.84

PhyloP100

0.37

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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rs885861

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over