11-57234352-C-T

Position:

• chr11-57234352-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
APLNR	NM_005161.6	c.*1510G>A		3_prime_UTR_variant	1/1	ENST00000606794.2	NP_005152.1
APLNR	NR_027991.2	n.1460-494G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APLNR	ENST00000606794	c.*1510G>A		3_prime_UTR_variant	1/1		NM_005161.6	ENSP00000475344.1
APLNR	ENST00000257254.3	n.*71-494G>A		intron_variant		1		ENSP00000257254.3

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37650 AN: 151898 Hom.: 5373 Cov.: 32

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: 48 AN: 136 Hom.: 11 Cov.: 0 AF XY: 0.357 AC XY: 35 AN XY: 98

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.366

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.248 AC: 37683 AN: 152016 Hom.: 5385 Cov.: 32 AF XY: 0.256 AC XY: 19019 AN XY: 74296

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.281

Alfa AF: 0.274 Hom.: 7374

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
DANN	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs2282623; hg19: chr11-57001826;