Variant X-129654413-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017413.5(APLN):c.67+151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 423,608 control chromosomes in the GnomAD database, including 13,784 homozygotes. There are 23,308 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7145 hom., 10181 hem., cov: 24)

Exomes 𝑓: 0.15 ( 6639 hom. 13127 hem. )

Consequence

APLN
NM_017413.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.218

Variant links:

Genes affected

APLN (HGNC:16665): (apelin) This gene encodes a peptide that functions as an endogenous ligand for the G-protein coupled apelin receptor. The encoded preproprotein is proteolytically processed into biologically active C-terminal peptide fragments. These peptide fragments activate different tissue specific signaling pathways that regulate diverse biological functions including fluid homeostasis, cardiovascular function and insulin secretion. This protein also functions as a coreceptor for the human immunodeficiency virus 1. [provided by RefSeq, Feb 2016]

APLN links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant X-129654413-T-C is Benign according to our data. Variant chrX-129654413-T-C is described in ClinVar as [Benign]. Clinvar id is 1253078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APLN	NM_017413.5 linkuse as main transcript	c.67+151A>G		intron_variant		ENST00000429967.3	NP_059109.3	Q9ULZ1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APLN	ENST00000429967.3 linkuse as main transcript	c.67+151A>G		intron_variant		1	NM_017413.5	ENSP00000391800.2		Q9ULZ1

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

33759

AN:

112117

Hom.:

7138

Cov.:

AF XY:

0.295

AC XY:

10139

AN XY:

34393

show subpopulations

Gnomad AFR

AF:

0.728

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.0979

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.0530

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0755

Gnomad OTH

AF:

0.285

GnomAD4 exome

AF:

0.147

AC:

45757

AN:

311441

Hom.:

6639

AF XY:

0.167

AC XY:

13127

AN XY:

78747

show subpopulations

Gnomad4 AFR exome

AF:

0.736

Gnomad4 AMR exome

AF:

0.269

Gnomad4 ASJ exome

AF:

0.0864

Gnomad4 EAS exome

AF:

0.794

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.0521

Gnomad4 NFE exome

AF:

0.0745

Gnomad4 OTH exome

AF:

0.196

GnomAD4 genome

AF:

0.301

AC:

33807

AN:

112167

Hom.:

7145

Cov.:

AF XY:

0.296

AC XY:

10181

AN XY:

34453

show subpopulations

Gnomad4 AFR

AF:

0.728

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.0979

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.249

Gnomad4 FIN

AF:

0.0530

Gnomad4 NFE

AF:

0.0755

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.171

Hom.:

1423

Bravo

AF:

0.343

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.71

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over