chr2-147900020-A-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001616.5(ACVR2A):c.528+122A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,886 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACVR2A
NM_001616.5 intron
NM_001616.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.00
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACVR2A | NM_001616.5 | c.528+122A>T | intron_variant | ENST00000241416.12 | |||
ACVR2A | NM_001278579.2 | c.528+122A>T | intron_variant | ||||
ACVR2A | NM_001278580.2 | c.204+122A>T | intron_variant | ||||
ACVR2A | XM_047446292.1 | c.204+122A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACVR2A | ENST00000241416.12 | c.528+122A>T | intron_variant | 1 | NM_001616.5 | P1 | |||
ACVR2A | ENST00000404590.1 | c.528+122A>T | intron_variant | 1 | P1 | ||||
ENST00000402410.2 | n.210+410T>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
ACVR2A | ENST00000535787.5 | c.204+122A>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 986398Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 493738
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151886Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74172
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at