Variant rs1128919 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001616.5(ACVR2A):c.354G>A(p.Pro118Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,611,270 control chromosomes in the GnomAD database, including 84,561 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 0.33 ( 8273 hom., cov: 31)

Exomes 𝑓: 0.32 ( 76288 hom. )

Consequence

ACVR2A
NM_001616.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.673

Variant links:

Genes affected

ACVR2A (HGNC:173): (activin A receptor type 2A) This gene encodes a receptor that mediates the functions of activins, which are members of the transforming growth factor-beta (TGF-beta) superfamily involved in diverse biological processes. The encoded protein is a transmembrane serine-threonine kinase receptor which mediates signaling by forming heterodimeric complexes with various combinations of type I and type II receptors and ligands in a cell-specific manner. The encoded type II receptor is primarily involved in ligand-binding and includes an extracellular ligand-binding domain, a transmembrane domain and a cytoplasmic serine-threonine kinase domain. This gene may be associated with susceptibility to preeclampsia, a pregnancy-related disease which can result in maternal and fetal morbidity and mortality. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jun 2013]

ACVR2A links:

ENSG00000223911 (HGNC:):

ENSG00000223911 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACVR2A	NM_001616.5 linkuse as main transcript	c.354G>A	p.Pro118Pro	synonymous_variant	3/11	ENST00000241416.12	NP_001607.1	P27037-1
ACVR2A	NM_001278579.2 linkuse as main transcript	c.354G>A	p.Pro118Pro	synonymous_variant	4/12		NP_001265508.1	P27037-1
ACVR2A	NM_001278580.2 linkuse as main transcript	c.30G>A	p.Pro10Pro	synonymous_variant	3/11		NP_001265509.1	P27037-2
ACVR2A	XM_047446292.1 linkuse as main transcript	c.30G>A	p.Pro10Pro	synonymous_variant	3/11		XP_047302248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACVR2A	ENST00000241416.12 linkuse as main transcript	c.354G>A	p.Pro118Pro	synonymous_variant	3/11	1	NM_001616.5	ENSP00000241416.7		P27037-1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49345

AN:

151700

Hom.:

8268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.311

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.349

GnomAD3 exomes

AF:

0.354

AC:

88511

AN:

250214

Hom.:

16400

AF XY:

0.348

AC XY:

47125

AN XY:

135380

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.459

Gnomad ASJ exome

AF:

0.346

Gnomad EAS exome

AF:

0.521

Gnomad SAS exome

AF:

0.310

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.350

GnomAD4 exome

AF:

0.319

AC:

465687

AN:

1459452

Hom.:

76288

Cov.:

AF XY:

0.318

AC XY:

231075

AN XY:

726038

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.452

Gnomad4 ASJ exome

AF:

0.341

Gnomad4 EAS exome

AF:

0.501

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.335

Gnomad4 NFE exome

AF:

0.306

Gnomad4 OTH exome

AF:

0.322

GnomAD4 genome

AF:

0.325

AC:

49394

AN:

151818

Hom.:

8273

Cov.:

AF XY:

0.327

AC XY:

24271

AN XY:

74188

show subpopulations

Gnomad4 AFR

AF:

0.299

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.328

Gnomad4 EAS

AF:

0.507

Gnomad4 SAS

AF:

0.311

Gnomad4 FIN

AF:

0.335

Gnomad4 NFE

AF:

0.314

Gnomad4 OTH

AF:

0.347

Alfa

AF:

0.322

Hom.:

9798

Bravo

AF:

0.333

Asia WGS

AF:

0.349

AC:

1215

AN:

3476

EpiCase

AF:

0.330

EpiControl

AF:

0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.36

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.36

Position offset: 19

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over