rs1128919
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001616.5(ACVR2A):c.354G>A(p.Pro118=) 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
NM_001616.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.673
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 -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 | UniProt |
---|---|---|---|---|---|---|---|
ACVR2A | NM_001616.5 | c.354G>A | p.Pro118= | synonymous_variant | 3/11 | ENST00000241416.12 | |
ACVR2A | NM_001278579.2 | c.354G>A | p.Pro118= | synonymous_variant | 4/12 | ||
ACVR2A | NM_001278580.2 | c.30G>A | p.Pro10= | synonymous_variant | 3/11 | ||
ACVR2A | XM_047446292.1 | c.30G>A | p.Pro10= | synonymous_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACVR2A | ENST00000241416.12 | c.354G>A | p.Pro118= | synonymous_variant | 3/11 | 1 | NM_001616.5 | P1 | |
ENST00000402410.2 | n.265C>T | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.325 AC: 49345AN: 151700Hom.: 8268 Cov.: 31
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GnomAD3 exomes AF: 0.354 AC: 88511AN: 250214Hom.: 16400 AF XY: 0.348 AC XY: 47125AN XY: 135380
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GnomAD4 exome AF: 0.319 AC: 465687AN: 1459452Hom.: 76288 Cov.: 32 AF XY: 0.318 AC XY: 231075AN XY: 726038
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GnomAD4 genome ? AF: 0.325 AC: 49394AN: 151818Hom.: 8273 Cov.: 31 AF XY: 0.327 AC XY: 24271AN XY: 74188
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 19
Find out detailed SpliceAI scores and Pangolin per-transcript scores at