rs10497189
Variant names:
Variant summary
Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
Benign
The NM_001111067.4(ACVR1):c.790+2076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,208 control chromosomes in the GnomAD database, including 447 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 0.069 ( 447 hom., cov: 32)
Consequence
ACVR1
NM_001111067.4 intron
NM_001111067.4 intron
Scores
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.570
Publications
8 publications found
Genes affected
ACVR1 (HGNC:171): (activin A receptor type 1) Activins are dimeric growth and differentiation factors which belong to the transforming growth factor-beta (TGF-beta) superfamily of structurally related signaling proteins. Activins signal through a heteromeric complex of receptor serine kinases which include at least two type I ( I and IB) and two type II (II and IIB) receptors. These receptors are all transmembrane proteins, composed of a ligand-binding extracellular domain with cysteine-rich region, a transmembrane domain, and a cytoplasmic domain with predicted serine/threonine specificity. Type I receptors are essential for signaling; and type II receptors are required for binding ligands and for expression of type I receptors. Type I and II receptors form a stable complex after ligand binding, resulting in phosphorylation of type I receptors by type II receptors. This gene encodes activin A type I receptor which signals a particular transcriptional response in concert with activin type II receptors. Mutations in this gene are associated with fibrodysplasia ossificans progressive. [provided by RefSeq, Jul 2008]
ACVR1 Gene-Disease associations (from GenCC):
- fibrodysplasia ossificans progressivaInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, ClinGen, PanelApp Australia, G2P
- congenital heart diseaseInheritance: AD Classification: LIMITED Submitted by: ClinGen
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript NM_001111067.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001111067.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ACVR1 | TSL:1 MANE Select | c.790+2076A>G | intron | N/A | ENSP00000405004.1 | Q04771 | |||
| ACVR1 | TSL:1 | c.790+2076A>G | intron | N/A | ENSP00000263640.3 | Q04771 | |||
| ACVR1 | TSL:1 | c.790+2076A>G | intron | N/A | ENSP00000387127.2 | Q04771 |
Frequencies
GnomAD3 genomes 0.0694 AC: 10560AN: 152090Hom.: 447 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
10560
AN:
152090
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0694 AC: 10560AN: 152208Hom.: 447 Cov.: 32 AF XY: 0.0660 AC XY: 4913AN XY: 74424 show subpopulations
GnomAD4 genome
AF:
AC:
10560
AN:
152208
Hom.:
Cov.:
32
AF XY:
AC XY:
4913
AN XY:
74424
show subpopulations
African (AFR)
AF:
AC:
884
AN:
41536
American (AMR)
AF:
AC:
655
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
370
AN:
3472
East Asian (EAS)
AF:
AC:
260
AN:
5178
South Asian (SAS)
AF:
AC:
315
AN:
4816
European-Finnish (FIN)
AF:
AC:
715
AN:
10600
Middle Eastern (MID)
AF:
AC:
17
AN:
294
European-Non Finnish (NFE)
AF:
AC:
7040
AN:
67994
Other (OTH)
AF:
AC:
151
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
498
996
1495
1993
2491
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
130
260
390
520
650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
197
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.
Other links and lift over
dbSNP: rs10497189 ;
hg19: chr2-158624804;