rs2159236
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001164458.2(ACTR3C):c.-52+3344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,110 control chromosomes in the GnomAD database, including 4,555 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 0.23 ( 4555 hom., cov: 33)
Consequence
ACTR3C
NM_001164458.2 intron
NM_001164458.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.328
Genes affected
ACTR3C (HGNC:37282): (actin related protein 3C) Predicted to enable ATP binding activity. Predicted to contribute to actin filament binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTR3C | NM_001164458.2 | c.-52+3344T>C | intron_variant | ENST00000683684.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTR3C | ENST00000683684.1 | c.-52+3344T>C | intron_variant | NM_001164458.2 | P1 | ||||
ACTR3C | ENST00000478393.5 | c.105+3344T>C | intron_variant | 1 | |||||
ACTR3C | ENST00000477367.1 | c.-52+2741T>C | intron_variant | 4 | |||||
ACTR3C | ENST00000477871.1 | c.246+3344T>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35588AN: 151992Hom.: 4563 Cov.: 33
GnomAD3 genomes
?
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35588
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151992
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.234 AC: 35589AN: 152110Hom.: 4555 Cov.: 33 AF XY: 0.239 AC XY: 17752AN XY: 74370
GnomAD4 genome
?
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35589
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152110
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33
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17752
AN XY:
74370
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1134
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at