rs3764955

chr2-147917228-G-Cchr2-147917228-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001616.5(ACVR2A):c.673-55G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,541,212 control chromosomes in the GnomAD database, including 72,097 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 0.26 (5956 hom., cov: 32)
  • Exomes 𝑓: 0.30 (66141 hom.)
• Consequence: ACVR2A NM_001616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ACVR2A	NM_001616.5	c.673-55G>C		intron_variant		ENST00000241416.12
ACVR2A	NM_001278579.2	c.673-55G>C		intron_variant
ACVR2A	NM_001278580.2	c.349-55G>C		intron_variant
ACVR2A	XM_047446292.1	c.349-55G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACVR2A	ENST00000241416.12	c.673-55G>C		intron_variant		1	NM_001616.5	P1
ACVR2A	ENST00000404590.1	c.673-55G>C		intron_variant		1		P1
ACVR2A	ENST00000535787.5	c.349-55G>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39455 AN: 151606 Hom.: 5960 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.304 AC: 422771 AN: 1389488 Hom.: 66141 AF XY: 0.304 AC XY: 208763 AN XY: 687032

Gnomad4 AFR exome AF: 0.0988

Gnomad4 AMR exome AF: 0.372

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.453

Gnomad4 SAS exome AF: 0.296

Gnomad4 FIN exome AF: 0.334

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.260 AC: 39468 AN: 151724 Hom.: 5956 Cov.: 32 AF XY: 0.263 AC XY: 19487 AN XY: 74120

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.295

Alfa AF: 0.283 Hom.: 820

Bravo AF: 0.257

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.9
Dann	Benign	0.66

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

Other links and lift over

dbSNP: rs3764955; hg19: chr2-148674797; COSMIC: COSV54020226;