NM_001616.5:c.56-10752C>T

Variant names:

• chr2-147885549-C-T
• rs1424941
• NM_001616.5:c.56-10752C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001616.5(ACVR2A):​c.56-10752C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,014 control chromosomes in the GnomAD database, including 1,917 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 0.14 (1917 hom., cov: 32)
• Consequence: ACVR2A NM_001616.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001616.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACVR2A	NM_001616.5	MANE Select	c.56-10752C>T		intron	N/A	NP_001607.1
	ACVR2A	NM_001278579.2		c.56-10752C>T		intron	N/A	NP_001265508.1
	ACVR2A	NM_001278580.2		c.-206-10815C>T		intron	N/A	NP_001265509.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACVR2A	ENST00000241416.12	TSL:1 MANE Select	c.56-10752C>T		intron	N/A	ENSP00000241416.7
	ACVR2A	ENST00000404590.1	TSL:1	c.56-10752C>T		intron	N/A	ENSP00000384338.1
	ACVR2A	ENST00000535787.5	TSL:2	c.-206-10815C>T		intron	N/A	ENSP00000439988.1

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21735 AN: 151896 Hom.: 1918 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0982

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.143 AC: 21728 AN: 152014 Hom.: 1917 Cov.: 32 AF XY: 0.138 AC XY: 10262 AN XY: 74304

African (AFR) AF: 0.0637 AC: 2642 AN: 41494

American (AMR) AF: 0.130 AC: 1989 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3466

East Asian (EAS) AF: 0.0978 AC: 507 AN: 5182

South Asian (SAS) AF: 0.152 AC: 734 AN: 4818

European-Finnish (FIN) AF: 0.0904 AC: 956 AN: 10572

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13163 AN: 67886

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.163 Hom.: 590

Bravo AF: 0.141

Asia WGS AF: 0.123 AC: 424 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.088
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1424941; hg19: chr2-148643118; COSMIC: COSV54018855;