rs7582403

Positions:

• chr2-147861185-A-G
• chr2-147861185-A-T

Variant summary

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

The NM_001616.5(ACVR2A):​c.55+15978A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,054 control chromosomes in the GnomAD database, including 10,544 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 0.35 (10544 hom., cov: 32)
• Consequence: ACVR2A NM_001616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACVR2A	NM_001616.5	c.55+15978A>G		intron_variant		ENST00000241416.12	NP_001607.1
ACVR2A	NM_001278579.2	c.55+15978A>G		intron_variant			NP_001265508.1
ACVR2A	NM_001278580.2	c.-207+16479A>G		intron_variant			NP_001265509.1
ACVR2A	XM_047446292.1	c.-270+16479A>G		intron_variant			XP_047302248.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACVR2A	ENST00000241416.12	c.55+15978A>G		intron_variant		1	NM_001616.5	ENSP00000241416	P1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53852 AN: 151936 Hom.: 10533 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.328

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53888 AN: 152054 Hom.: 10544 Cov.: 32 AF XY: 0.364 AC XY: 27080 AN XY: 74308

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.333

Alfa AF: 0.306 Hom.: 1277

Bravo AF: 0.328

Asia WGS AF: 0.471 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.4
DANN	Benign	0.59

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: rs7582403; hg19: chr2-148618754;