Genetic Variant APLNR:c.*1510G>A (chr11-57234352-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_005161.6(APLNR):c.*1510G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,152 control chromosomes in the GnomAD database, including 5,396 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 0.25 ( 5385 hom., cov: 32)

Exomes 𝑓: 0.35 ( 11 hom. )

Consequence

APLNR
NM_005161.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.504

Publications

20 publications found

Variant links:

Genes affected

APLNR (HGNC:339): (apelin receptor) This gene encodes a member of the G protein-coupled receptor gene family. The encoded protein is related to the angiotensin receptor, but is actually an apelin receptor that inhibits adenylate cyclase activity and plays a counter-regulatory role against the pressure action of angiotensin II by exerting hypertensive effect. It functions in the cardiovascular and central nervous systems, in glucose metabolism, in embryonic and tumor angiogenesis and as a human immunodeficiency virus (HIV-1) coreceptor. Two transcript variants resulting from alternative splicing have been identified. [provided by RefSeq, Jul 2009]

APLNR links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APLNR	NM_005161.6 link	c.*1510G>A		3_prime_UTR_variant	Exon 1 of 1	ENST00000606794.2	NP_005152.1
APLNR	NR_027991.2 link	n.1460-494G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APLNR	ENST00000606794.2 link	c.*1510G>A		3_prime_UTR_variant	Exon 1 of 1	6	NM_005161.6	ENSP00000475344.1
APLNR	ENST00000257254.3 link	n.*71-494G>A		intron_variant	Intron 1 of 1	1		ENSP00000257254.3

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37650

AN:

151898

Hom.:

5373

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.276

GnomAD4 exome

AF:

0.353

AC:

AN:

136

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.366

AC:

AN:

112

Other (OTH)

AF:

0.300

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:

0.248

AC:

37683

AN:

152016

Hom.:

5385

Cov.:

AF XY:

0.256

AC XY:

19019

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.109

AC:

4510

AN:

41504

American (AMR)

AF:

0.325

AC:

4955

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1182

AN:

3468

East Asian (EAS)

AF:

0.398

AC:

2047

AN:

5140

South Asian (SAS)

AF:

0.446

AC:

2143

AN:

4806

European-Finnish (FIN)

AF:

0.345

AC:

3654

AN:

10586

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18263

AN:

67946

Other (OTH)

AF:

0.281

AC:

592

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1388

2776

4163

5551

6939

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.269

Hom.:

8898

Bravo

AF:

0.241

Asia WGS

AF:

0.447

AC:

1552

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.9

(source)

DANN

Benign

0.58

PhyloP100

0.50

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over