GeneBe

rs1441735

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001613.4(ACTA2):​c.990+949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control

Consequence

ACTA2
NM_001613.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.619

Publications

3 publications found
Variant links:
Genes affected
ACTA2 (HGNC:130): (actin alpha 2, smooth muscle) This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, integrity, and intercellular signaling. The encoded protein is a smooth muscle actin that is involved in vascular contractility and blood pressure homeostasis. Mutations in this gene cause a variety of vascular diseases, such as thoracic aortic disease, coronary artery disease, stroke, and Moyamoya disease, as well as multisystemic smooth muscle dysfunction syndrome. [provided by RefSeq, Sep 2017]
STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
ACTA2-AS1 (HGNC:45169): (ACTA2 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001613.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ACTA2
NM_001613.4
MANE Select
c.990+949C>T
intron
N/ANP_001604.1
ACTA2
NM_001141945.3
c.990+949C>T
intron
N/ANP_001135417.1
ACTA2
NM_001320855.2
c.990+949C>T
intron
N/ANP_001307784.1

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ACTA2
ENST00000224784.10
TSL:1 MANE Select
c.990+949C>T
intron
N/AENSP00000224784.6
STAMBPL1
ENST00000371927.7
TSL:2
c.1254+14676G>A
intron
N/AENSP00000360995.3
ACTA2
ENST00000713598.1
c.1032+949C>T
intron
N/AENSP00000518894.1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
149382
Hom.:
0
Cov.:
31
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
149382
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
72892
African (AFR)
AF:
0.00
AC:
0
AN:
40616
American (AMR)
AF:
0.00
AC:
0
AN:
15164
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3290
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5156
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4590
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10400
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
66868
Other (OTH)
AF:
0.00
AC:
0
AN:
2074
Alfa
AF:
0.00
Hom.:
364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
5.5
DANN
Benign
0.90
PhyloP100
-0.62

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

Other links and lift over

dbSNP: rs1441735; hg19: chr10-90696869; API