rs2113794

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001616.5(ACVR2A):​c.55+20201T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,968 control chromosomes in the GnomAD database, including 11,886 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 0.39 ( 11886 hom., cov: 32)

Consequence

ACVR2A
NM_001616.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACVR2ANM_001616.5 linkuse as main transcriptc.55+20201T>G intron_variant ENST00000241416.12 NP_001607.1
ACVR2ANM_001278579.2 linkuse as main transcriptc.55+20201T>G intron_variant NP_001265508.1
ACVR2ANM_001278580.2 linkuse as main transcriptc.-207+20702T>G intron_variant NP_001265509.1
ACVR2AXM_047446292.1 linkuse as main transcriptc.-270+20702T>G intron_variant XP_047302248.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACVR2AENST00000241416.12 linkuse as main transcriptc.55+20201T>G intron_variant 1 NM_001616.5 ENSP00000241416 P1P27037-1

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58847
AN:
151850
Hom.:
11873
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.282
Gnomad AMI
AF:
0.396
Gnomad AMR
AF:
0.398
Gnomad ASJ
AF:
0.284
Gnomad EAS
AF:
0.379
Gnomad SAS
AF:
0.503
Gnomad FIN
AF:
0.552
Gnomad MID
AF:
0.222
Gnomad NFE
AF:
0.423
Gnomad OTH
AF:
0.353
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
58896
AN:
151968
Hom.:
11886
Cov.:
32
AF XY:
0.396
AC XY:
29444
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.281
Gnomad4 AMR
AF:
0.399
Gnomad4 ASJ
AF:
0.284
Gnomad4 EAS
AF:
0.380
Gnomad4 SAS
AF:
0.503
Gnomad4 FIN
AF:
0.552
Gnomad4 NFE
AF:
0.423
Gnomad4 OTH
AF:
0.358
Alfa
AF:
0.413
Hom.:
1679
Bravo
AF:
0.365
Asia WGS
AF:
0.476
AC:
1654
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.64
DANN
Benign
0.49

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.

Other links and lift over

dbSNP: rs2113794; hg19: chr2-148622977; API